Showing preview only (9,222K chars total). Download the full file or copy to clipboard to get everything.
Repository: lgmgeo/AnnotSV
Branch: master
Commit: 64faaf546e03
Files: 279
Total size: 8.7 MB
Directory structure:
gitextract_mvkn4kk8/
├── .gitignore
├── License.txt
├── Makefile
├── README.md
├── Scoring_Criteria_AnnotSV_v3.4.xlsx
├── bin/
│ ├── AnnotSV
│ └── INSTALL_annotations.sh
├── changeLog.txt
├── commandLineOptions.txt
├── etc/
│ └── AnnotSV/
│ ├── application.properties
│ └── configfile
├── share/
│ ├── bash/
│ │ └── AnnotSV/
│ │ ├── checkPhenoGeniusCliInstall.sh
│ │ └── searchForAFreePortNumber.bash
│ ├── doc/
│ │ └── AnnotSV/
│ │ ├── Example/
│ │ │ ├── README.commands
│ │ │ ├── test1.annotated.tsv
│ │ │ ├── test1.annotated.variantconvert.log
│ │ │ ├── test1.annotated.vcf
│ │ │ ├── test1.bed
│ │ │ ├── test2.annotated.tsv
│ │ │ ├── test2.annotated.variantconvert.log
│ │ │ ├── test2.annotated.vcf
│ │ │ └── test2.vcf
│ │ ├── annotations.md
│ │ ├── quickstart.md
│ │ ├── ranking.md
│ │ └── webserver_overview.md
│ └── tcl/
│ └── AnnotSV/
│ ├── AnnotSV-benignsv.tcl
│ ├── AnnotSV-candidategenes.tcl
│ ├── AnnotSV-clingen.tcl
│ ├── AnnotSV-closestgenes.tcl
│ ├── AnnotSV-config.tcl
│ ├── AnnotSV-cosmic.tcl
│ ├── AnnotSV-cytoband.tcl
│ ├── AnnotSV-encodeblacklist.tcl
│ ├── AnnotSV-exac.tcl
│ ├── AnnotSV-exomiser.tcl
│ ├── AnnotSV-extann.tcl
│ ├── AnnotSV-filteredVCF.tcl
│ ├── AnnotSV-gap.tcl
│ ├── AnnotSV-gccontent.tcl
│ ├── AnnotSV-gencc.tcl
│ ├── AnnotSV-general.tcl
│ ├── AnnotSV-genes.tcl
│ ├── AnnotSV-haploinsufficiency.tcl
│ ├── AnnotSV-help.tcl
│ ├── AnnotSV-loeuf-pLI.tcl
│ ├── AnnotSV-ncbi.tcl
│ ├── AnnotSV-omim.tcl
│ ├── AnnotSV-pathogenicsnvindel.tcl
│ ├── AnnotSV-pathogenicsv.tcl
│ ├── AnnotSV-phenogenius.tcl
│ ├── AnnotSV-ranking.tcl
│ ├── AnnotSV-regulatoryelements.tcl
│ ├── AnnotSV-repeat.tcl
│ ├── AnnotSV-segdup.tcl
│ ├── AnnotSV-tad.tcl
│ ├── AnnotSV-userBED.tcl
│ ├── AnnotSV-variantconvert.tcl
│ ├── AnnotSV-vcf.tcl
│ ├── AnnotSV-write.tcl
│ ├── Scripts/
│ │ └── lift_Over_a_BED_file.tcl
│ └── tcllib/
│ ├── csv/
│ │ ├── csv.tcl
│ │ └── pkgIndex.tcl
│ ├── http/
│ │ ├── autoproxy.tcl
│ │ └── pkgIndex.tcl
│ ├── json/
│ │ ├── json.tcl
│ │ ├── json_tcl.tcl
│ │ ├── json_write.tcl
│ │ ├── jsonc.tcl
│ │ └── pkgIndex.tcl
│ └── tar/
│ ├── pkgIndex.tcl
│ └── tar.tcl
└── tests/
└── AnnotSV/
├── README
├── scripts/
│ ├── check_all_public_test_directory.sh
│ ├── check_end_values.tcl
│ ├── check_includeCI.tcl
│ ├── complete_KnotAnnotSV_YAML_test.tcl
│ └── cutWithColumnNames.tcl
├── test_01_configfile/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_02_HG00096/
│ ├── command_Tcl.sh
│ ├── command_python.sh
│ └── input/
│ ├── HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.bed
│ └── HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.vcf
├── test_03_CDSandTxCoverage/
│ ├── command_Tcl.sh
│ └── input/
│ ├── control_9deletions_FCGR3A_NM_000569.bed
│ └── test_tcl.annotated.tsv.truth.sauv
├── test_04_ExternalBEDannotationFiles/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ ├── user_FtIncludedInSV.bed
│ └── user_SVincludedInFt.bed
├── test_05_BEDwithoutHeader/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ └── test.withoutHeader.bed
├── test_06_VCFfromLumpy/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.DEL.DUP.vcf
│ ├── test1.csv
│ └── test1.vcf
├── test_07_RegulatoryElement/
│ ├── command_Tcl.sh
│ └── input/
│ ├── candidateGenesFile.txt
│ ├── delMEF2C.bed
│ └── delSOX9.bed
├── test_08_largeSV/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_09_InsertionInAgene/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_10_BadVCFformat/
│ ├── command_Tcl.sh
│ └── input/
│ ├── testTRA.vcf
│ └── testVCFwithoutHeader.vcf
├── test_11_RamTracking/
│ ├── README
│ ├── commandAnnotSV.sh
│ └── command_Tcl.sh
├── test_12_SpaceSeparatedBED/
│ ├── command_Tcl.sh
│ └── input/
│ ├── space-separated.NA.bed
│ ├── space-separated.bed
│ └── tab-separated.bed
├── test_13_txFile/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.check1.bed
│ ├── test.check2.vcf
│ ├── txFile.check1.txt
│ ├── txFile.check2.txt
│ └── txFile.check3.txt
├── test_14_candidateGenesFile/
│ ├── 5
│ ├── command_Tcl.sh
│ └── input/
│ ├── candidateGenesFile.txt
│ └── test.bed
├── test_15_EmptyVCF/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.vcf
├── test_16_reciprocalYes/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ ├── test.vcf
│ └── user_SVincludedInFt.bed
├── test_17_rankFiltering/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_18_VCFwithBrackets/
│ ├── command_Tcl.sh
│ └── input/
│ ├── INPUT_gridss_germline_output.sv.vcf
│ └── triplesvmerge.vcf
├── test_19_Mouse/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.RE.bed
│ └── test.bed
├── test_20_MitochondrialSV/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_21_ExternalGeneAnnotationFile/
│ ├── command_Tcl.sh
│ └── input/
│ ├── configfile
│ ├── input.bed
│ └── user_annotations.tsv
├── test_22_knotAnnotSV_41SV/
│ ├── command_Tcl.sh
│ └── input/
│ ├── config_AnnotSV.tmp.yaml
│ ├── test.41_SV.bed
│ └── test.7_SV.bed
├── test_23_Exomiser/
│ ├── command_Tcl.sh
│ └── input/
│ ├── GRCh37-1SV.vcf
│ ├── GRCh37-multiSV.vcf
│ ├── GRCh38-1SV.vcf
│ └── GRCh38-multiSV.vcf
├── test_24_HtzCompound/
│ ├── command_Tcl.sh
│ └── input/
│ ├── 3samples.severalSV.vcf
│ ├── 3samples.snvindel.vcf
│ ├── 3samples.theSV.vcf
│ ├── 3samples.theSnvindel.vcf
│ ├── configfile
│ ├── test1.SV.bed
│ ├── test1.SV.vcf
│ ├── test1.SV.withoutGT.vcf
│ ├── test1.snvindel.vcf
│ └── test1.snvindel.withoutGT.vcf
├── test_25_big-ref-alt/
│ ├── command_Tcl.sh
│ └── input/
│ └── input_1-big-ref.vcf
├── test_26_HtzHomCounts_deletionFiltering/
│ ├── README
│ ├── command_Tcl.sh
│ └── input/
│ ├── 3samples.SV.vcf
│ ├── 3samples.extract-HG00096.snvindel.vcf
│ ├── SV.bed
│ ├── extract-HG00096.vcf
│ └── extract-tutu.vcf
├── test_27_Samples_ID/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test-withoutHeader.bed
│ ├── test.bed
│ └── test.vcf
├── test_28_SVsharingTheSameCoordinatesButWithDifferentSVTYPE/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_29_distNearestSS/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test1.vcf
│ ├── test2.bed
│ ├── test3.bed
│ ├── test4.bed
│ ├── test5.bed
│ └── test6.bed
├── test_30_Ranking/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_31_Cytoband/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_32_metrics/
│ ├── command_Tcl.sh
│ └── input/
│ └── input.bed
├── test_33_webSiteExample/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_34_bracketedToAngularNotations/
│ ├── README
│ ├── Rodrigo_tests_ignore/
│ │ ├── Difficult/
│ │ │ ├── README
│ │ │ ├── test.vcf
│ │ │ └── test_difficult.vcf
│ │ ├── Outputs/
│ │ │ ├── command_20_square-bracketed-inv2.annotated.tsv
│ │ │ ├── input_OnlyTheReciprocalBND_square-bracketed-tra1_1.annotated.tsv
│ │ │ └── input_OnlyTheReciprocalBND_square-bracketed-tra1_2.annotated.tsv
│ │ ├── README
│ │ ├── output.csv
│ │ ├── severalSVTYPE-square-bracketed.vcf
│ │ ├── test_paired.vcf
│ │ ├── tra.output.csv
│ │ └── tra.vcf
│ ├── command_Tcl.sh
│ └── input/
│ ├── input-angle-bracketed-del_1.vcf
│ ├── input-angle-bracketed-del_partial_pass.vcf
│ ├── input-angle-bracketed-dup.vcf
│ ├── input-angle-bracketed-empty_del.vcf
│ ├── input-angle-bracketed-ins_by_gridss.vcf
│ ├── input-angle-bracketed-inv1.vcf
│ ├── input-angle-bracketed-inv2.vcf
│ ├── input-angle-bracketed-tra1.vcf
│ ├── input-angle-bracketed-tra2.vcf
│ ├── input-del_1.bed
│ ├── input-del_partial_pass.bed
│ ├── input-dup.bed
│ ├── input-empty_del.bed
│ ├── input-ins_by_gridss.bed
│ ├── input-inv1.bed
│ ├── input-square-bracketed-del_1.vcf
│ ├── input-square-bracketed-del_partial_pass.vcf
│ ├── input-square-bracketed-del_unordered.vcf
│ ├── input-square-bracketed-dup.vcf
│ ├── input-square-bracketed-empty_del.vcf
│ ├── input-square-bracketed-ins_by_gridss.vcf
│ ├── input-square-bracketed-inv1.vcf
│ ├── input-square-bracketed-inv2.vcf
│ ├── input-square-bracketed-inv3.vcf
│ ├── input-square-bracketed-tra1.vcf
│ ├── input-square-bracketed-tra2.vcf
│ ├── input-tra1.bed
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_1.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_partial_pass.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_unordered.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-dup.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-empty_del.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-ins_by_gridss.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-inv1.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-inv2.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-tra1_1.vcf
│ └── input_OnlyTheReciprocalBND_square-bracketed-tra1_2.vcf
├── test_35_phenogenius/
│ ├── command_Tcl.sh
│ └── input/
│ ├── PKD1.bed
│ └── test.bed
├── test_36_chm13/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_37_SVLEN/
│ ├── README
│ ├── command_Tcl.sh
│ └── input/
│ ├── input-angle-bracketed-del.vcf
│ ├── input-angle-bracketed-dup.vcf
│ ├── input-angle-bracketed-inv.vcf
│ ├── input-angle-bracketed-tra.vcf
│ ├── input-del.bed
│ ├── input-dup.bed
│ ├── input-ins_by_gridss.bed
│ ├── input-inv.bed
│ ├── input-square-bracketed-del.vcf
│ ├── input-square-bracketed-dup.vcf
│ ├── input-square-bracketed-ins_by_gridss.vcf
│ ├── input-square-bracketed-inv.vcf
│ ├── input-square-bracketed-tra.vcf
│ └── input-tra.bed
├── test_38_samePosINSwithDiffInsertedSeq/
│ ├── README
│ ├── command_Tcl.sh
│ ├── input/
│ │ ├── test_INS_1.vcf
│ │ ├── test_INS_2.vcf
│ │ └── test_INS_3.vcf
│ ├── test_INS_1.annotated.tsv
│ ├── test_INS_2.annotated.tsv
│ └── test_INS_3.annotated.tsv
└── test_39_breakpointProximity/
├── command_Tcl.sh
└── input/
├── A.bed
└── B.bed
================================================
FILE CONTENTS
================================================
================================================
FILE: .gitignore
================================================
.pdm.toml
# tests
etc/AnnotSV/configfile.minAnnotation
etc/AnnotSV/application.properties.2007
etc/AnnotSV/application.properties.1902
# Annotations
share/AnnotSV/Annotations_Human/
share/AnnotSV/Annotations_Mouse/
share/AnnotSV/Annotations_Exomiser/
# Python reimplementation of AnnotSV
# + PhenoGenius install
share/python3/annotsv/
src/annotsv/
Python/
share/python3/phenogeniuscli/
# Exomiser:
# File share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar is 114.75 MB; this exceeds GitHub's file size limit of 100.00 MB
# => Downloaded with the Makefile
share/AnnotSV/jar/exomiser-rest-prioritiser-14.1.0.jar
# Unit tests
tests/AnnotSV/privateTest_*
tests/AnnotSV/test_*/command_Tcl.log
tests/AnnotSV/test_*/output/
tests/AnnotSV/ToDo
tests/AnnotSV/check_all_public_test_directory.log
tests/AnnotSV/test_11_RamTracking/ramAnnotSV-*-ram.txt
# VariantConvert
share/python3/variantconvert/pipinstall.flag
share/python3/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from*local.json
share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from*local.json
share/python3/variantconvert/src/variantconvert/configs/CHM13/annotsv3_from*local.json
share/python3/variantconvert/src/variantconvert/__pycache__/
share/python3/variantconvert/src/variantconvert/__pycache__/*.pyc
share/python3/variantconvert/src/variantconvert/converters/__pycache__/
share/python3/variantconvert/src/variantconvert/converters/__pycache__/*.pyc
share/python3/variantconvert/src/variantconvert.egg-info/
================================================
FILE: License.txt
================================================
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
To "modify" a work means to copy from or adapt all or part of the work
in a fashion requiring copyright permission, other than the making of an
exact copy. The resulting work is called a "modified version" of the
earlier work or a work "based on" the earlier work.
A "covered work" means either the unmodified Program or a work based
on the Program.
To "propagate" a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a
computer or modifying a private copy. Propagation includes copying,
distribution (with or without modification), making available to the
public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
1. Source Code.
The "source code" for a work means the preferred form of the work
for making modifications to it. "Object code" means any non-source
form of a work.
A "Standard Interface" means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that
is widely used among developers working in that language.
The "System Libraries" of an executable work include anything, other
than the work as a whole, that (a) is included in the normal form of
packaging a Major Component, but which is not part of that Major
Component, and (b) serves only to enable use of the work with that
Major Component, or to implement a Standard Interface for which an
implementation is available to the public in source code form. A
"Major Component", in this context, means a major essential component
(kernel, window system, and so on) of the specific operating system
(if any) on which the executable work runs, or a compiler used to
produce the work, or an object code interpreter used to run it.
The "Corresponding Source" for a work in object code form means all
the source code needed to generate, install, and (for an executable
work) run the object code and to modify the work, including scripts to
control those activities. However, it does not include the work's
System Libraries, or general-purpose tools or generally available free
programs which are used unmodified in performing those activities but
which are not part of the work. For example, Corresponding Source
includes interface definition files associated with source files for
the work, and the source code for shared libraries and dynamically
linked subprograms that the work is specifically designed to require,
such as by intimate data communication or control flow between those
subprograms and other parts of the work.
The Corresponding Source need not include anything that users
can regenerate automatically from other parts of the Corresponding
Source.
The Corresponding Source for a work in source code form is that
same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of
copyright on the Program, and are irrevocable provided the stated
conditions are met. This License explicitly affirms your unlimited
permission to run the unmodified Program. The output from running a
covered work is covered by this License only if the output, given its
content, constitutes a covered work. This License acknowledges your
rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not
convey, without conditions so long as your license otherwise remains
in force. You may convey covered works to others for the sole purpose
of having them make modifications exclusively for you, or provide you
with facilities for running those works, provided that you comply with
the terms of this License in conveying all material for which you do
not control copyright. Those thus making or running the covered works
for you must do so exclusively on your behalf, under your direction
and control, on terms that prohibit them from making any copies of
your copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under
the conditions stated below. Sublicensing is not allowed; section 10
makes it unnecessary.
3. Protecting Users' Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological
measure under any applicable law fulfilling obligations under article
11 of the WIPO copyright treaty adopted on 20 December 1996, or
similar laws prohibiting or restricting circumvention of such
measures.
When you convey a covered work, you waive any legal power to forbid
circumvention of technological measures to the extent such circumvention
is effected by exercising rights under this License with respect to
the covered work, and you disclaim any intention to limit operation or
modification of the work as a means of enforcing, against the work's
users, your or third parties' legal rights to forbid circumvention of
technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program's source code as you
receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice;
keep intact all notices stating that this License and any
non-permissive terms added in accord with section 7 apply to the code;
keep intact all notices of the absence of any warranty; and give all
recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey,
and you may offer support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to
produce it from the Program, in the form of source code under the
terms of section 4, provided that you also meet all of these conditions:
a) The work must carry prominent notices stating that you modified
it, and giving a relevant date.
b) The work must carry prominent notices stating that it is
released under this License and any conditions added under section
7. This requirement modifies the requirement in section 4 to
"keep intact all notices".
c) You must license the entire work, as a whole, under this
License to anyone who comes into possession of a copy. This
License will therefore apply, along with any applicable section 7
additional terms, to the whole of the work, and all its parts,
regardless of how they are packaged. This License gives no
permission to license the work in any other way, but it does not
invalidate such permission if you have separately received it.
d) If the work has interactive user interfaces, each must display
Appropriate Legal Notices; however, if the Program has interactive
interfaces that do not display Appropriate Legal Notices, your
work need not make them do so.
A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
"aggregate" if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms
of sections 4 and 5, provided that you also convey the
machine-readable Corresponding Source under the terms of this License,
in one of these ways:
a) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by the
Corresponding Source fixed on a durable physical medium
customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by a
written offer, valid for at least three years and valid for as
long as you offer spare parts or customer support for that product
model, to give anyone who possesses the object code either (1) a
copy of the Corresponding Source for all the software in the
product that is covered by this License, on a durable physical
medium customarily used for software interchange, for a price no
more than your reasonable cost of physically performing this
conveying of source, or (2) access to copy the
Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the
written offer to provide the Corresponding Source. This
alternative is allowed only occasionally and noncommercially, and
only if you received the object code with such an offer, in accord
with subsection 6b.
d) Convey the object code by offering access from a designated
place (gratis or for a charge), and offer equivalent access to the
Corresponding Source in the same way through the same place at no
further charge. You need not require recipients to copy the
Corresponding Source along with the object code. If the place to
copy the object code is a network server, the Corresponding Source
may be on a different server (operated by you or a third party)
that supports equivalent copying facilities, provided you maintain
clear directions next to the object code saying where to find the
Corresponding Source. Regardless of what server hosts the
Corresponding Source, you remain obligated to ensure that it is
available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided
you inform other peers where the object code and Corresponding
Source of the work are being offered to the general public at no
charge under subsection 6d.
A separable portion of the object code, whose source code is excluded
from the Corresponding Source as a System Library, need not be
included in conveying the object code work.
A "User Product" is either (1) a "consumer product", which means any
tangible personal property which is normally used for personal, family,
or household purposes, or (2) anything designed or sold for incorporation
into a dwelling. In determining whether a product is a consumer product,
doubtful cases shall be resolved in favor of coverage. For a particular
product received by a particular user, "normally used" refers to a
typical or common use of that class of product, regardless of the status
of the particular user or of the way in which the particular user
actually uses, or expects or is expected to use, the product. A product
is a consumer product regardless of whether the product has substantial
commercial, industrial or non-consumer uses, unless such uses represent
the only significant mode of use of the product.
"Installation Information" for a User Product means any methods,
procedures, authorization keys, or other information required to install
and execute modified versions of a covered work in that User Product from
a modified version of its Corresponding Source. The information must
suffice to ensure that the continued functioning of the modified object
code is in no case prevented or interfered with solely because
modification has been made.
If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
part of a transaction in which the right of possession and use of the
User Product is transferred to the recipient in perpetuity or for a
fixed term (regardless of how the transaction is characterized), the
Corresponding Source conveyed under this section must be accompanied
by the Installation Information. But this requirement does not apply
if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has
been installed in ROM).
The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or updates
for a work that has been modified or installed by the recipient, or for
the User Product in which it has been modified or installed. Access to a
network may be denied when the modification itself materially and
adversely affects the operation of the network or violates the rules and
protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
unpacking, reading or copying.
7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders of
that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or
requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or
authors of the material; or
e) Declining to grant rights under trademark law for use of some
trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that
material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
those licensors and authors.
All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
additional terms that apply to those files, or a notice indicating
where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions;
the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
modify it is void, and will automatically terminate your rights under
this License (including any patent licenses granted under the third
paragraph of section 11).
However, if you cease all violation of this License, then your
license from a particular copyright holder is reinstated (a)
provisionally, unless and until the copyright holder explicitly and
finally terminates your license, and (b) permanently, if the copyright
holder fails to notify you of the violation by some reasonable means
prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.
Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
modify any covered work. These actions infringe copyright if you do
not accept this License. Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
================================================
FILE: Makefile
================================================
############################################################################################################
# AnnotSV 3.5.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
# Copyright (C) 2017-present Veronique Geoffroy (veronique.geoffroy@inserm.fr) #
# #
# This is part of AnnotSV source code. #
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License #
# as published by the Free Software Foundation; either version 3 #
# of the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; If not, see <http://www.gnu.org/licenses/>. #
############################################################################################################
SHELL = /usr/bin/env bash
DESTDIR ?=
PREFIX ?= /usr/local
INSTALLDIR1 := $(shell readlink -f "$(DESTDIR)$(PREFIX)")
INSTALLDIR2 := $(shell readlink -f "$(DESTDIR).")
BINDIR := $(PREFIX)/bin
ETCDIR := $(PREFIX)/etc
SHAREDIR := $(PREFIX)/share
DOCDIR := $(SHAREDIR)/doc
BASHDIR := $(SHAREDIR)/bash
TESTSDIR := $(PREFIX)/tests
TCLVERSION := tcl$(shell echo 'puts $${tcl_version};exit 0' | tclsh)
TCLDIRDISTRIBUTED := share/tcl
TCLDIR := $(SHAREDIR)/$(TCLVERSION)
PYTHONDIR := $(SHAREDIR)/python3
ANNOTSV := AnnotSV
JARDIR := $(SHAREDIR)/$(ANNOTSV)/jar
VERSION := 3.5.8
HUMANVERSION := 3.5
MOUSEVERSION := 3.4.2
RM := /bin/rm
RMDIR := /bin/rmdir
MKDIR := install -d
MV := /bin/mv
CP := install -p -m 0644
CPDIR := /bin/cp -r
CHMOD := /bin/chmod -R 777
CONFIGFILE := etc/$(ANNOTSV)/configfile
MAKEFILE := Makefile
PROPERTIES := etc/$(ANNOTSV)/application.properties
BASH_SCRIPTS := $(shell find share/bash/$(ANNOTSV)/ -name '*.bash' 2> /dev/null)
DOCUMENTATIONS := $(shell find License.txt changeLog.txt commandLineOptions.txt README.AnnotSV_*.pdf 2> /dev/null)
VC_FLAG := $(DESTDIR)$(PYTHONDIR)/variantconvert/pipinstall.flag
VC_VERSION := 2.0.1
VC_CONFIGDIR := $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs
USEANNODIR := #flag whether separate annotation resources directory needed (e.g. for HPC environvment)
EXRP_FILE := #optional filepath for previously downloaded rest-prioritiser
# make install
.PHONY: install
ifeq ('$(INSTALLDIR1)' , '$(INSTALLDIR2)')
all: install-display install-documentationlight install-variantconvert install-done
install: install-display install-documentationlight install-variantconvert install-done
install-exomiser: install-exomiser-1 install-exomiser-3
else
all: install-display install-configfile install-makefile install-executable install-tcl-toolbox install-bash-toolbox install-doc install-others-doc install-variantconvert install-done
install: install-display install-configfile install-makefile install-executable install-tcl-toolbox install-bash-toolbox install-doc install-others-doc install-variantconvert install-done
install-exomiser: install-exomiser-1 install-exomiser-2 install-exomiser-3
endif
# For all PREFIX
install-display:
@echo ""
@echo "Installation of $(ANNOTSV)-$(VERSION):"
@echo "----------------------------"
@echo DESTDIR=$(DESTDIR)
@echo PREFIX=$(PREFIX)
@echo TCLVERSION=$(TCLVERSION)
# For PREFIX==.
install-documentationlight: $(DOCUMENTATIONS)
@echo ""
@if [ -n "$^" ]; then \
$(MV) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV); \
fi
@if [ -d "$(TCLDIRDISTRIBUTED)" ]; then \
$(MV) "$(TCLDIRDISTRIBUTED)" "$(TCLDIR)"; \
fi
# For PREFIX!=.
install-configfile: $(CONFIGFILE)
@echo ""
@echo "Configfile configuration"
@echo "------------------------"
$(MKDIR) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
install -p -m 0755 $(CONFIGFILE) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
# For PREFIX!=.
install-makefile: $(MAKEFILE)
@echo ""
@echo "Makefile installation"
@echo "---------------------"
install -p -m 0755 $(MAKEFILE) $(DESTDIR)$(PREFIX)
# For PREFIX!=.
install-executable:
@echo ""
@echo "Executable installation"
@echo "-----------------------"
$(MKDIR) $(DESTDIR)$(BINDIR)
install -p -m 0755 bin/AnnotSV $(DESTDIR)$(BINDIR)
# For PREFIX!=.
install-tcl-toolbox:
@echo ""
@echo "Tcl scripts installation"
@echo "------------------------"
$(MKDIR) $(DESTDIR)$(TCLDIR)/$(ANNOTSV)
cd share/tcl ; tar cf - $(ANNOTSV) | tar xf - -C $(DESTDIR)$(TCLDIR)/
# For all PREFIX
install-variantconvert:
@echo ""
@echo "variantconvert installation"
@echo "---------------------------"
@if [ -d $(DESTDIR)$(PYTHONDIR)/variantconvert ]; then \
echo "variantconvert directory found; purging locally before re-installing."; \
rm -rf $(DESTDIR)$(PYTHONDIR)/variantconvert/; \
fi
git clone --branch $(VC_VERSION) https://github.com/SamuelNicaise/variantconvert.git $(DESTDIR)$(PYTHONDIR)/variantconvert/
touch $(VC_FLAG)
chmod 777 $(VC_FLAG)
pip3 install -e $(DESTDIR)$(PYTHONDIR)/variantconvert/. > ./tmp.variantconvert.txt 2>&1 \
|| pip install -e $(DESTDIR)$(PYTHONDIR)/variantconvert/. >> ./tmp.variantconvert.txt 2>&1 \
|| python -m pip install -e $(DESTDIR)$(PYTHONDIR)/variantconvert/. >> ./tmp.variantconvert.txt 2>&1 \
|| rm -f $(VC_FLAG)
@if [ -f $(VC_FLAG) ]; then \
echo "variantconvert installed"; \
$(CHMOD) ./tmp.variantconvert.txt; \
rm -f ./tmp.variantconvert.txt; \
$(CHMOD) $(VC_CONFIGDIR); \
$(MV) $(VC_CONFIGDIR)/hs1 $(VC_CONFIGDIR)/CHM13; \
for f in $(VC_CONFIGDIR)/CHM13/annotsv*; do \
case "$$f" in \
*.json) \
sed -i 's/"##contig=<ID=chr/"##contig=<ID=/g' "$$f" ;; \
esac; \
done; \
# Creation of the "*.local.json" files for Conda use. \
for genome in GRCh37 GRCh38 CHM13; do \
for source in bed vcf; do \
for type in combined full fullsplit; do \
echo "touch $(VC_CONFIGDIR)/$$genome/annotsv3_from_$$source.$$type.local.json" ; \
touch $(VC_CONFIGDIR)/$$genome/annotsv3_from_$$source.$$type.local.json; \
$(CHMOD) $(VC_CONFIGDIR)/$$genome/annotsv3_from_$$source.$$type.local.json; \
done; \
done; \
done; \
else \
echo "variantconvert not installed"; \
fi
# For PREFIX!=.
install-bash-toolbox: $(BASH_SCRIPTS)
@echo ""
@echo "Bash scripts installation"
@echo "-------------------------"
$(MKDIR) $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
$(CP) $^ $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
# For PREFIX!=.
install-doc: $(DOCUMENTATIONS)
@echo ""
@echo "Documentations installation"
@echo "---------------------------"
$(MKDIR) $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
$(CP) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
# For PREFIX!=.
install-others-doc: share/doc/$(ANNOTSV)/Example
$(CPDIR) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
# For all PREFIX
install-done:
@echo ""
@echo "Done"
@echo ""
@echo "WARNING: Annotations need to be installed:"
@echo "make DESTDIR=$(DESTDIR) PREFIX=$(PREFIX) install-human-annotation"
@echo "make DESTDIR=$(DESTDIR) PREFIX=$(PREFIX) install-mouse-annotation"
# make install_organism_annotations
install-all-annotations: install-human-annotation install-mouse-annotation
install-human-annotation: install-exomiser $(if $(USEANNODIR),,Annotations_Human_$(HUMANVERSION).tar.gz)
ifndef USEANNODIR
@echo ""
@echo "Installation of human annotation:"
@echo ""
tar -xf Annotations_Human_$(HUMANVERSION).tar.gz -C $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
$(RM) -rf Annotations_Human_$(HUMANVERSION).tar.gz
$(CHMOD) $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_*
@echo ""
@echo "--> Human annotation installed"
else
@echo ""
@echo "Flag for custom annotationDir; skipping local install of human annotations"
@echo ""
endif
# For PREFIX==.
install-exomiser-1: $(if $(USEANNODIR),,2406_phenotype.zip)
@echo ""
@echo "Installation of Exomiser data:"
@echo ""
ifndef USEANNODIR
$(MKDIR) -p $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406
unzip 2406_phenotype.zip -d $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2406/
$(RM) -rf 2406_phenotype.zip
else
@echo ""
@echo "Flag for custom annotationDir; skipped Exomiser phenotypes local installation"
@echo ""
endif
$(MKDIR) -p $(DESTDIR)$(JARDIR)
ifndef EXRP_FILE
curl -C - -LO https://github.com/exomiser/Exomiser/releases/download/14.1.0/exomiser-rest-prioritiser-14.1.0.jar
install -p -m 0755 exomiser-rest-prioritiser-14.1.0.jar $(DESTDIR)$(JARDIR)/
$(RM) exomiser-rest-prioritiser-14.1.0.jar
else
@echo "Custom rest-priotiser path provided; creating symlink"
ln -sf $(EXRP_FILE) $(DESTDIR)$(JARDIR)/$(notdir $(EXRP_FILE))
endif
# For PREFIX!=.
install-exomiser-2:
install -D -p -m 0755 $(PROPERTIES) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
# For PREFIX==.
install-exomiser-3:
@echo ""
@echo "--> Exomiser data installed"
install-mouse-annotation: $(if $(USEANNODIR),,Annotations_Mouse_$(MOUSEVERSION).tar.gz)
ifndef USEANNODIR
@echo ""
@echo "Installation of mouse annotation:"
@echo ""
$(MKDIR) $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
tar -xf Annotations_Mouse_$(MOUSEVERSION).tar.gz -C $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
$(RM) -rf Annotations_Mouse_$(MOUSEVERSION).tar.gz
@echo ""
@echo "--> Mouse annotation installed"
else
@echo ""
@echo "Flag for custom annotationDir; skipping local install of mouse annotations"
@echo ""
endif
Annotations_%.tar.gz:
@echo ""
@echo "Download AnnotSV supporting data files:"
@echo ""
curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/$@
%_phenotype.zip:
@echo ""
@echo "Download Exomiser supporting data files:"
@echo ""
curl -C - -LO https://data.monarchinitiative.org/exomiser/data/$@
# make uninstall
.PHONY: uninstall
ifeq ('$(PREFIX)' , '/usr/local')
uninstall: uninstall1 uninstall4
else ifeq ('$(INSTALLDIR1)' , '$(INSTALLDIR2)')
uninstall: uninstall1 uninstall2 uninstall4
else
uninstall: uninstall1 uninstall2 uninstall3 uninstall4
endif
uninstall1:
@echo ""
@echo "Uninstalling of $(ANNOTSV)"
@echo "------------------------"
$(RM) -f $(DESTDIR)$(BINDIR)/$(ANNOTSV)
$(RM) -f $(DESTDIR)$(BINDIR)/INSTALL_annotations.sh
$(RM) -f $(DESTDIR)$(BINDIR)/INSTALL_code.sh
$(RM) -rf $(DESTDIR)$(TCLDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PYTHONDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PYTHONDIR)/variantconvert
$(RM) -rf $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(TESTSDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PREFIX)/Makefile
$(RM) -rf $(DESTDIR)$(PREFIX)/README.md
$(RM) -rf $(DESTDIR)$(PREFIX)/Scoring_Criteria_AnnotSV_*.xlsx
$(RM) -rf $(DESTDIR)$(PREFIX)/.git
$(RM) -rf $(DESTDIR)$(PREFIX)/.gitignore
$(RM) -rf $(DESTDIR)$(PREFIX)/tmp.variantconvert.txt
uninstall2:
$(RMDIR) --ignore-fail-on-non-empty $(DESTDIR)$(BINDIR) $(DESTDIR)$(BASHDIR) $(DESTDIR)$(TCLDIR) $(DESTDIR)$(PYTHONDIR) $(DESTDIR)$(DOCDIR) $(DESTDIR)$(SHAREDIR) $(DESTDIR)$(ETCDIR) $(DESTDIR)$(TESTSDIR)
uninstall3:
$(RMDIR) --ignore-fail-on-non-empty $(DESTDIR)$(PREFIX)
uninstall4:
@echo ""
@echo "Done"
================================================
FILE: README.md
================================================
<p align="center">
<img src="share/doc/AnnotSV/Images/AnnotSV_logo.png" width="500">
<br />
<div align="center">
<h1 style="font-weight: bold">An integrated tool for Structural Variations annotation and ranking</h1>
</div>
<br />
# Table of contents
- ## AnnotSV Annotations Engine
- ### [README](README.AnnotSV_3.5.7.pdf)
- ### [Getting Started](share/doc/AnnotSV/quickstart.md)
- ### [Ranking](share/doc/AnnotSV/ranking.md)
- ### [Annotations](share/doc/AnnotSV/annotations.md)
- ## AnnotSV Webserver
- ### [Overview](share/doc/AnnotSV/webserver_overview.md)
- ## AnnotSV issues
<b>Please detail your request when <a href="https://github.com/lgmgeo/AnnotSV/issues" target="_blank">reporting a bug</a>:</b>
- Give the version of AnnotSV and the command line used
- Add/join an input file that allow to reproduce the bug
- Give all the information that could have an impact on the bug reported (modifications made in the installation or in the annotation files)
- Specify if you use Singularity...
<br />
# Collaborative work
Anyone interested in implementing new annotations/features in AnnotSV?
Thanks to the [AnnotSV user community](https://lbgi.fr/AnnotSV/acknowledgments):
- Bugs could be tackled efficiently
- New ideas could be investigated faster
We look forward to the opportunity to work together, feel free to fork the page if you want to help :-)
================================================
FILE: bin/AnnotSV
================================================
#!/usr/bin/env tclsh
############################################################################################################
# AnnotSV 3.5.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
# Copyright (C) 2017-present Veronique Geoffroy (veronique.geoffroy@inserm.fr) #
# #
# This is part of AnnotSV source code. #
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License #
# as published by the Free Software Foundation; either version 3 #
# of the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; If not, see <http://www.gnu.org/licenses/>. #
############################################################################################################
# non-zero exit codes --> usually interpreted as error cases
# zero exit code --> Terminate the process without error
# exit <=> exit 0 (default)
global g_AnnotSV
proc getScriptDirectory {} {
set scriptFilePath [file normalize [info script]]
set scriptDir [file dirname $scriptFilePath]
return $scriptDir
}
#if {[info exists env(ANNOTSV)]} {
# regsub "/$" $env(ANNOTSV) "" env(ANNOTSV)
#}
#set ANNOTSVinstallDir [file normalize "$env(ANNOTSV)"]
# Setting of g_AnnotSV(installDir), g_AnnotSV(etcDir), g_AnnotSV(docDir), g_AnnotSV(tclDir) and g_AnnotSV(bashDir):
set binDirFromScript [getScriptDirectory]
regsub "/bin$" $binDirFromScript "" binDirFromScript
set g_AnnotSV(installDir) "$binDirFromScript"
set g_AnnotSV(etcDir) "$g_AnnotSV(installDir)/etc/AnnotSV"
set g_AnnotSV(docDir) "$g_AnnotSV(installDir)/share/doc/AnnotSV"
set tclVersion [info tclversion]
set g_AnnotSV(tclDir) "$g_AnnotSV(installDir)/share/tcl${tclVersion}/AnnotSV"
if {![file exists $g_AnnotSV(tclDir)]} {
set g_AnnotSV(tclDir) "$g_AnnotSV(installDir)/share/tcl/AnnotSV"
}
set g_AnnotSV(bashDir) "$g_AnnotSV(installDir)/share/bash/AnnotSV"
# g_AnnotSV(annotationsDir) is set to "$g_AnnotSV(installDir)/share/AnnotSV" in AnnotSV-config.tcl
# Setting of "auto_path" for the use of the Tcl packages added in AnnotSV
set auto_path [linsert $::auto_path 0 $g_AnnotSV(tclDir)/tcllib]
source $g_AnnotSV(tclDir)/AnnotSV-benignsv.tcl
source $g_AnnotSV(tclDir)/AnnotSV-candidategenes.tcl
source $g_AnnotSV(tclDir)/AnnotSV-clingen.tcl
source $g_AnnotSV(tclDir)/AnnotSV-closestgenes.tcl
source $g_AnnotSV(tclDir)/AnnotSV-config.tcl
source $g_AnnotSV(tclDir)/AnnotSV-cosmic.tcl
source $g_AnnotSV(tclDir)/AnnotSV-cytoband.tcl
source $g_AnnotSV(tclDir)/AnnotSV-encodeblacklist.tcl
source $g_AnnotSV(tclDir)/AnnotSV-exac.tcl
source $g_AnnotSV(tclDir)/AnnotSV-exomiser.tcl
source $g_AnnotSV(tclDir)/AnnotSV-extann.tcl
source $g_AnnotSV(tclDir)/AnnotSV-filteredVCF.tcl
source $g_AnnotSV(tclDir)/AnnotSV-gap.tcl
source $g_AnnotSV(tclDir)/AnnotSV-gccontent.tcl
source $g_AnnotSV(tclDir)/AnnotSV-gencc.tcl
source $g_AnnotSV(tclDir)/AnnotSV-general.tcl
source $g_AnnotSV(tclDir)/AnnotSV-genes.tcl
source $g_AnnotSV(tclDir)/AnnotSV-haploinsufficiency.tcl
source $g_AnnotSV(tclDir)/AnnotSV-help.tcl
source $g_AnnotSV(tclDir)/AnnotSV-loeuf-pLI.tcl
source $g_AnnotSV(tclDir)/AnnotSV-ncbi.tcl
source $g_AnnotSV(tclDir)/AnnotSV-omim.tcl
source $g_AnnotSV(tclDir)/AnnotSV-pathogenicsv.tcl
source $g_AnnotSV(tclDir)/AnnotSV-pathogenicsnvindel.tcl
source $g_AnnotSV(tclDir)/AnnotSV-phenogenius.tcl
source $g_AnnotSV(tclDir)/AnnotSV-regulatoryelements.tcl
source $g_AnnotSV(tclDir)/AnnotSV-ranking.tcl
source $g_AnnotSV(tclDir)/AnnotSV-repeat.tcl
source $g_AnnotSV(tclDir)/AnnotSV-segdup.tcl
source $g_AnnotSV(tclDir)/AnnotSV-tad.tcl
source $g_AnnotSV(tclDir)/AnnotSV-userBED.tcl
source $g_AnnotSV(tclDir)/AnnotSV-variantconvert.tcl
source $g_AnnotSV(tclDir)/AnnotSV-vcf.tcl
source $g_AnnotSV(tclDir)/AnnotSV-write.tcl
# Setting of g_AnnotSV(Version):
if {![info exists g_AnnotSV(Version)]} {
set configFile "$g_AnnotSV(tclDir)/AnnotSV-config.tcl"
foreach L [LinesFromFile $configFile] {
if {[regexp "^# AnnotSV (\[0-9\]+.\[0-9\]+(.\[0-9\]+)?)" $L match version]} {
set g_AnnotSV(Version) "$version"
break
}
}
}
if {![info exists g_AnnotSV(Version)]} {
set g_AnnotSV(Version) "X.X"
}
puts "AnnotSV $g_AnnotSV(Version)"
if {[regexp "\-version|\-Version" $argv]} {
exit
}
puts ""
puts "Copyright (C) 2017-current GEOFFROY Veronique"
puts ""
puts "Please feel free to create a Github issue for any suggestions or bug reports (https://github.com/lgmgeo/AnnotSV/issues)"
puts ""
puts "Tcl/Tk version: $tclVersion"
puts ""
puts "Application name used:"
puts "$g_AnnotSV(installDir)\n\n"
set tclVersion [split $tclVersion "."]
if {[lindex $tclVersion 0] < 8 || ([lindex $tclVersion 0] eq 8 && [lindex $tclVersion 1] < 5)} {
puts "AnnotSV requires a release of the Tcl distribution starting with version 8.5."
puts "(AnnotSV has not been tested with lower version)"
}
## No argument given:
if {$argv == ""} {
puts "Arguments are missing see help below\n"
showHelp; exit 0
}
## Needing help?
if {[regexp -nocase "help" $argv]} {showHelp; exit 0}
## Downloading configuration:
configureAnnotSV $argv
## Depending of the VCF or BED input format:
if {[regexp -nocase "\\.vcf(.gz)?$" $g_AnnotSV(SVinputFile)]} {
## SVinputfile is a VCF?
## -> need to be formated in bed
set g_AnnotSV(bedFile) [VCFsToBED "$g_AnnotSV(SVinputFile)"]
} else {
## SVinputfile is a BED
set g_AnnotSV(bedFile) $g_AnnotSV(SVinputFile)
regsub -nocase ".bed$" $g_AnnotSV(bedFile) ".header.tsv" BEDinputHeaderFile
if {"$g_AnnotSV(bedFile)" ne "$BEDinputHeaderFile"} {file delete -force $BEDinputHeaderFile}
createBEDinputHeaderFile
addNAinSamplesIDbedCol
}
## Check VariantConvert configuration:
######################################
checkVariantconvertConfigfile
## Genes annotations:
#####################
puts "...checking the annotation data sources ([clock format [clock seconds] -format "%B %d %Y - %H:%M"])"
# Annotation of genes depending of the transcripts (RefSeq or ENSEMBL) ?
if {$g_AnnotSV(tx) eq "RefSeq"} {
checkGenesRefSeqFile
} else {
checkGenesENSEMBLfile
}
# Annotation with GenCC?
checkGenCCgeneFile
# Annotation with OMIM?
checkNCBIandHGNC
memorizeGeneNameAlias
checkOMIMfile
checkMorbidfile
# Annotation with HI (Haploinsufficiency)?
checkHIfile
# Annotation with ClinGen?
checkClinGenFile
# Annotation with Exomiser?
# checkNCBI (done with OMIM)
checkExomiserInstallation
# Annotation with PhenoGenius?
checkPhenoGeniusCli
# Annotation with LOEUF
checkLOEUFfile
## SVincludedInFt:
##################
# Annotations with benign genes or genomic regions?
checkBenignFiles
checkOverlappedGenesBenignFiles
# Annotation with GeneIntolerance (ExAC)?
checkGeneIntoleranceFile
checkCNVintoleranceFile
## Breakpoint annotations:
##########################
# Annotation with GC content?
checkFASTAfiles
# Annotation with Repeat?
checkRepeatFile
# Annotation with Segmental Duplication?
checkSegDupFile
# Annotation with Gap?
checkGapFile
# Annotation with ENCODE blacklist?
checkENCODEblacklistFile
# Cytoband
checkCytoband
## FtIncludedInSV annotations:
##############################
# Annotations with pathogenic genes or genomic regions?
checkPathogenicFiles
# Annotations with pathogenic SNV/indel?
checkPathoSNVindelFile
# Annotation with Regulatory Elements?
checkPromoterFile
checkEAfiles
checkGHfiles
checkMiRTargetLinkFiles
checkABCfiles
checkMPRAfiles
# Annotation with TAD?
checkTADfiles
# Annotation with COSMIC?
checkCOSMICfile
# Users BED regions annotations files:
# (from $ANNOTSV/share/AnnotSV/Annotations_$g_AnnotSV(organism)/Users/GRCh*/*ncludedIn*/*.bed)
##############################################################################################
checkUsersBED
# Users Gene-based annotation files:
# (from $ANNOTSV/Annotations_$g_AnnotSV(organism)/*/ and from user command lines "-externalGeneFiles")
######################################################################################################
# g_AnnotSV(extann) has been initialized in AnnotSV-config.tcl
# g_AnnotSV(extann) will be completed in AnnotSV-exomiser.tcl
set geneBasedDir "$g_AnnotSV(annotationsDir)/Annotations_$g_AnnotSV(organism)/Gene-based"
foreach annotFile [glob -nocomplain $geneBasedDir/*/*.tsv] {
if {[regexp "_DGV_samplesInStudies.tsv$" $annotFile]} {continue}
lappend g_AnnotSV(extann) $annotFile
}
foreach annotFile [glob -nocomplain $geneBasedDir/*/*.tsv.gz] {
lappend g_AnnotSV(extann) $annotFile
}
set userDir "$g_AnnotSV(annotationsDir)/Annotations_$g_AnnotSV(organism)/Users/"
foreach annotFile [glob -nocomplain $userDir/*.tsv] {
lappend g_AnnotSV(extann) $annotFile
}
foreach annotFile [glob -nocomplain $userDir/*.tsv.gz] {
lappend g_AnnotSV(extann) $annotFile
}
foreach annotFile $g_AnnotSV(externalGeneFiles) {
lappend g_AnnotSV(extann) $annotFile
}
# Depending of the organism, genes based annotation can be absent:
if {$g_AnnotSV(extann) eq ""} {set g_AnnotSV(geneBasedAnn) 0} else {set g_AnnotSV(geneBasedAnn) 1}
# DISPLAY
puts ""
puts "...listing arguments"
puts "\t******************************************"
puts "\tAnnotSV has been run with these arguments:"
puts "\t******************************************"
set lKey [array names g_AnnotSV]
foreach key [lsort $lKey] {
if {[regexp "ABCann|GHann|MPRAann|EAann|Ann|bashDir|bedFile|docDir|etcDir|extann|installDir|outputColHeader|ranking|genes|samplesidTSVcol|svtTSVcol|tclDir|userDir|Version$" $key]} {continue}
if {$g_AnnotSV($key) eq ""} {continue}
puts "\t-$key $g_AnnotSV($key)"
}
puts "\t******************************************\n"
# Annotation with the gene track
genesAnnotation
OrganizeAnnotation
if {[regexp "\\.bed$" $g_AnnotSV(SVinputFile)]} {
file delete -force $BEDinputHeaderFile
}
puts "\n...AnnotSV is done with the analysis ([clock format [clock seconds] -format "%B %d %Y - %H:%M"])"
================================================
FILE: bin/INSTALL_annotations.sh
================================================
#!/bin/bash
############################################################
# Installing AnnotSV human annotations in a local directory
############################################################
# USAGE:
########
# INSTALL_annotations.sh "Version of AnnotSV human annotation" "Version of Exomiser phenotype annotations"
# AIM:
######
# Download Exomiser and AnnotSV annotations to be used with the "-annotationsDir" option
# CONTEXT:
##########
# To work with bioconda/docker/singularity, AnnotSV couldn't contain the annotations in the recipe (that would make the recipe very large, which is a bad practice in bioconda)
# Users need to download the annotation files once and pass the directory to AnnotSV at runtime with the "-annotationsDir" option.
mkdir AnnotSV_annotations
cd AnnotSV_annotations
# AnnotSV annotations
echo ""
echo "Download AnnotSV supporting data files:"
echo ""
curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_$1.tar.gz
tar -xf Annotations_Human_$1.tar.gz -C ./
rm -rf Annotations_Human_$1.tar.gz
# Exomiser
echo ""
echo "Download Exomiser supporting data files:"
echo ""
curl -C - -LO https://data.monarchinitiative.org/exomiser/data/$2_phenotype.zip
unzip $2_phenotype.zip -d Annotations_Exomiser/$2/
rm -rf 2406_phenotype.zip
chmod -R 777 ./Annotations_*
================================================
FILE: changeLog.txt
================================================
############################################################################################################
# AnnotSV 3.5.8 #
# #
# An integrated tool for Structural Variations annotation #
# #
# Copyright (C) 2017-present Veronique Geoffroy (veronique.geoffroy@inserm.fr) #
# #
############################################################################################################
For more details, please see the README file.
April, 16, 2026 AnnotSV version 3.5.8
- Add a fix for the install (issue 328)
April, 14, 2026 AnnotSV version 3.5.7
- Add a new annotation mode: BNDproximity
This mode allows matching SV with user-provided BED features based on breakpoint proximity rather than interval overlap.
A feature is reported when both its start and end coordinates are within a user-defined distance of the SV breakpoints.
=> A new parameter is available: -breakpointProximity (default: 100 bp)
- Improve the rules for determining the frameshift status
April, 02, 2026 AnnotSV version 3.5.6
- Allow to customize the weights of AnnotSV ranking criteria in the configfile
- Add of the "bracketedAltMode" option
Defines how bracketed ALT values in VCF are interpreted:
The SV can be considered as DEL, DUP, INS or INV, or considered as BND (TRA is always reported as BND)
Values: ALL (default, infer all bracketed ALT as DEL, DUP, INS or INV)
BND (treat all bracketed ALT as BND)
comma-separated SVTYPE values among DEL, DUP, INS or INV (infer only selected SVTYPE; e.g.: "DEL,DUP". Others are treated as BND)
- Add of the "bracketedAltMaxSize" option
Define a maximum SV length (Mb) for SVTYPE inference from bracketed ALT values. Above 10 Mb (default), bracketed ALT is treated as BND.
- Return 2 unique AnnotSV_Ids for two insertions located at the same position but with different inserted sequences (issue 324)
- Add bugfix for the interpretation of square-bracketed DUP fields in the VCF (those containing the start of the duplicated sequence)
- Add bugfix in the Makefile for bioconda (issue 307#issuecomment-4054614762)
March, 03, 2026 AnnotSV version 3.5.5
- Improvements of the Makefile (by @drew-sinha)
add flag for annotation file download, expose path to rest-prioritiser
Annotations installion script no longer relies on AnnotSV make/install
application.properties now has version filled in programmatically
Non-destructive install; fix git install to allow repeats (still doesn't install for system apk builds)
February, 27, 2026 AnnotSV version 3.5.4
- Improvements of the Makefile (by Bradford Powell @bpow-patch)
Update install-exomiser-2 command in Makefile to support PREFIX
September, 12, 2025, AnnotSV version 3.5.3
- Improvments of the INSTALL_annotations.sh file to be version-controlled (issue 296)
August, 29, 2025, AnnotSV version 3.5.2
- Improvements in the GeneHancer section (several sources authorized for the downloaded files)
- Improvements in the tests section (test_37_SVLEN) + Makefile
August, 21, 2025, AnnotSV version 3.5.1
- Add bugfix concerning the SV_length (issue 295)
- Update the exomiser application.properties file
- Update the variantconvert install
- Update the Copyright output
July, 17, 2025, AnnotSV version 3.5
- Add the T2T-CHM13v2.0 human annotations
- Update GRCh38 and GRCh37 human annotations
- Update the Exomiser install
- Add bugfix concerning the AnnotSV_ranking_criteria
- Add bugfix concerning the naming of temporary files. Add the pid in the file names
- Add bugfix concerning the boundary mismatch for ACMG scores
- Improvements in the tests section
- Add the PacBio-CoLoRS Benign SV annotations (Long Read Sequencing Database, GRCh38, CHM13)
- Return 2 unique AnnotSV_Ids for two translocations starting at the same position but ending at a different position
March, 06, 2025, AnnotSV version 3.4.6
- Update the PhenoGenius install (Use of the client repo https://github.com/kyauy/PhenoGeniusCli: v.1.1.3) (issue 274)
February, 27, 2025, AnnotSV version 3.4.5
- Update the PhenoGenius install (Use of the client repo https://github.com/kyauy/PhenoGeniusCli: v.1.1.2)
- Add the "-missingGTinSamplesid" option (to report or not sample IDs with missing alleles in the GT field (./. or .|.) in the "Samples_ID" output field)
- Fix a bug to set start position when converting from 0-based to 1-based format in some rare special cases (issue 266)
- Fix a bug concerning Mouse annotations (issue 257)
September, 05, 2024, AnnotSV version 3.4.4
- Temporary fix for issues #239 and #250 (wrong PRDM10 line in the GenCC file)
=> Code to be removed after updating annotations
August, 29, 2024, AnnotSV version 3.4.3
- New definition of alias gene symbols used in OMIM annotation files.
Keep only aliases found with the NCBI_gene_ID and validated with genomic locations
- Add a new check for the variantconvert configuration (issue 246)
- Fix a bug in the AnnotSV_ID setting when POS (e.g. 1) is contained in CHROM (e.g. 1)
May, 14, 2024, AnnotSV version 3.4.2
- Fix a bug when setting the cytoband annotation for large SV (issue 234)
- Update the mm39 repeat annotations (issue 225)
May, 03, 2024, AnnotSV version 3.4.1
- Update of the variantconvert distribution (2.0.1 installed)
Add of the "-variantconvertMode" option (to choose the variantconvert conversion mode)
- Mouse annotation update (Add GRCm39/mm39 annotations)
- Remove typos in the ranking explanation
- Check the user bedtools version
- Restricts the number of RE_gene features to 50, RE with "PhenoGenius specificity = "A" or Exomiser gene score > 0.7" are displayed first.
- Integrate all the gene symbols for OMIM morbid annotations
- Improve the creation of the benign dataset (gnomAD, 1000g and HPRC)
- Add log files for the PhenoGenius install
February, 16, 2024, AnnotSV version 3.4
- Human annotation update
- Add new regulatory elements annotations:
- Activity-by-Contact (ABC) model annotations (doi: 10.1038/s41586-021-03446-x)
- Massively Parallel Reporter assays (MPRA) annotations (doi: 10.1038/s41467-019-11526-w)
- Add novel benign SV annotation sources:
- from gnomad v4 (GRCh38) (issue 201)
- from the Human Pangenome Reference Consortium (HPRC) dataset (PACBIO long reads, GRCh38 only) (issue 202)
- from dbVar (NCBI’s database of genomic structural variation)
- Add new phenotype prioritization method: PhenoGenius (Yauy et al., 2023, doi: 10.1101/2022.07.29.22278181)
- Add 3 new features: PhenoGenius_score, PhenoGenius_phenotype and PhenoGenius_specificity
- Add 4 new features:
- Closest_left and Closest_right
AnnotSV expands the SV up to 5 megabases in both direction (left and right) and then tries to find neighboring genes
In both directions, the closest gene to the SV is reported
- NCBI_gene_ID
- Tx_version (transcript version)
- Gene names are now sorted by genomic coordinates and no longer sorted alphabetically ("Gene_name" feature)
- Fix a bug when setting the cytoband annotation (issue 210)
- Fix misleading OMIM annotation (issues 156, 132)
- Update of the Makefile
- Update of the "contact" recommendations in output (from email to GitHub)
- Reorganization of the GitHub .md files
January, 15, 2024, AnnotSV version 3.3.9
- Fix a bug when setting the "hpoVersion" variable (issue 207)
December, 22, 2023, AnnotSV version 3.3.8
- Add of 34 unit tests
November, 03, 2023, AnnotSV version 3.3.7
- Fix a domain error (issue 199)
- Include code to allow FranceGenRef benign SV annotation (856 WGS with ancestries in different regions of France)
WARNING: not supplied as part of the AnnotSV sources.
- Optimize access to the exomiser application properties file for use with singularity/bioconda
- Allow uppercase file extensions (".VCF", ".BED" or ".VCF.GZ")
- Use the new format of the COSMIC data source
- Update of the documentation in $ANNOTSV/docs/
- Update of the documentation to install AnnotSV human annotations in a local directory (INSTALL_annotations.sh)
- Optimize a regexp
- Fix variantconvert file name
June, 01, 2023, AnnotSV version 3.3.6
- Add bug fix concerning some INV bracketed. The second breakend notation (which is just the reciprocal of the first) is now always identified as the mate breakend.
- Sample IDs with missing alleles in the GT fields ("./." or ".|.") are now reported in the "Samples_ID" output field
- Refactor variantconvert code
- Allow description of REF/ALT values in SV input files with lowercase ACGT
- Update of the .gitignore file
- Add bug fix to report only a subset of the annotation columns provided by AnnotSV
- Add of warning messages for the ranking (in case of missing required annotations)
- Update the display of the default command line
April, 14, 2023, AnnotSV version 3.3.5
- Add documentation on the "-includeCI" option
- Add bugfix for variantconvert use in GRCh38 (when setting the REF in the VCF output file)
- Add bugfix during the install (depending on the environment)
April, 07, 2023, AnnotSV version 3.3.4
- Among the “po_P_*_*” features, redundancy is now removed ONLY from “po_P_*_phen” and “po_P_*_hpo”.
=> AnnotSV keeps now the correspondence between “po_P_*_source”, “po_P_*_coord” and “po_P_*_percent” features.
- Improvment of the running time (code part: SV partially overlapping with an established benign region)
- Update of the Makefile (variantconvert install)
- Remove requirement for ANNOTSV environment variable
- Add of the "INSTALL_code.sh" and "INSTALL_annotations.sh" bash files (for a basic manual installation)
- Add a check of the "#CHROM" header line
- Add of the "-variantconvertDir" option (path of the variantconvert directory). By default, the variantconvert tool distributed by annotSV is used.
March, 30, 2023, AnnotSV version 3.3.3
- Add bugfix for large input file
March, 28, 2023, AnnotSV version 3.3.2
- Add bugfix for SV partially overlapping with an established benign region. Ranking Impact
- Improve the 40 criteria (Loss) in the SV ranking
- Restrict the number of "po_B_*_someG_*" features to 20
March, 24, 2023, AnnotSV version 3.3.1
- Add bugfix with the use of the SVminSize option
- Report the minimal LOEUF value (among those of all overlapped genes) in the SV full length annotation
- Update of the variantconvert distribution (1.2.2 installed)
March, 23, 2023, AnnotSV version 3.3
- Add bugfix regarding genomic start coordinates. TSV and VCF output files are now both 1-based, with inclusive-end (whatever the input file format)
- Add interpretation of the square-bracketed SV breakend notations within the VCF.
This new module relies on the homogenization rules provided within the variant-extractor tool developed by Rodrigo Martín.
- Update of the variantconvert distribution (1.2.1 installed)
- Automation of the variantconvert module installaton
- Reformat of the unannotated.tsv file
- Add of the .gitignore file
- VCF format handling update. According to the VCF 4.4 specification, the SVTYPE has now been deprecated (due to redundancy with ALT).
The SV type is now extracted primarily from the ALT column, then from the SVTYPE field in the INFO column if available.
- Add bugfix for the TAD annotations update process
January, 31, 2023, AnnotSV version 3.2.3
- Report of the "Samples_ID" column in ALL outputs (default, sample = NA) (required by variantconvert)
- Add the creation of a VCF output file from a "BED" SV input file. The "-vcf" and "-svtBEDcol" options are required.
- In VCF output, the GT is set to “1/.” for each SV if the GT is not given in input (BED input file)
- Add bugfix concerning Mouse annotation
January, 06, 2023, AnnotSV version 3.2.2
- Add bugfix concerning the use of variantconvert to create the VCF output file (GRCh37/GRCh38, configfiles)
December, 21, 2022, AnnotSV version 3.2.1
- Add bugfix concerning the partial overlap with some specific dbVar SV (same start and end locations)
December 13, 2022, AnnotSV version 3.2
- Add of a new output format: VCF
- Add partial overlap annotation:
- Add 4 benign gain SV annotation: po_B_gain_allG_source, po_B_gain_allG_coord, po_B_gain_someG_source, po_B_gain_someG_coord
- Add 4 benign loss SV annotation: po_B_loss_allG_source, po_B_loss_allG_coord, po_B_loss_someG_source, po_B_loss_someG_coord
- Add 5 pathogenic gain SV annotation: po_P_gain_phen, po_P_gain_hpo, po_P_gain_source, po_P_gain_coord, po_P_gain_percent
- Add 5 pathogenic loss SV annotation: po_P_loss_phen, po_P_loss_hpo, po_P_loss_source, po_P_loss_coord, po_P_loss_percen
- Add the 2B, 2G and 4O criteria (Loss) in the SV ranking
- Add the 2B, 2C, 2F, 2G and 4O criteria (Gain) in the SV ranking
- Update of the "make uninstall"
September 12, 2022, AnnotSV version 3.1.3
- Human annotation update
- Use of the new ClinGen data source format ("OMIM ID" no longer reported)
- Removing of the DDG2P gene annotations (to avoid redundancy with GenCC)
- Documentation update
July 10, 2022, AnnotSV version 3.1.2
- Add important bugfix concerning the GRCh38 coordinates of the morbid genes
- Add bugfix concerning some Overlapped_CDS_percent values
November 25, 2021, AnnotSV version 3.1.1
- Add bugfix when setting the ANNOTSV global environmental variable with a final "/"
- Documentation update
November 08, 2021, AnnotSV version 3.1
- Change the -genomeBuild default value to "GRCh38" (instead of GRCh37)
- Use boolean values (instead of "yes"/"no") for the following option values: -candidateGenesFiltering, -includeCI, -overwrite, -reciprocal, -REreport, -REselect1 and -REselect2
- Add the Children’s Mercy Research Institute Benign SV annotations (n=502 WGS)
- Add the GenCC database for Gene-Disease relationship annotations
- Add CytoBand annotation
- Add novel regulatory element annotation:
- Add miRNA annotation (from miRTargetLink)
- Complete the RE_gene column output (the regulated gene name is detailed with more information: candidate gene annotation
and data sources (RefSeq, ENSEMBL, EnhancerAtlas, GeneHancer and/or miRTargetLink))
- Add the "-REselect1" and "-REselect2" options to filter the RE_gene output
- Update the benign SV annotation method:
- Add the "-benignAF" option to change the allele frequency threshold used to select the benign SV in the data sources
- Add 4 annotation columns: B_gain_AFmax, B_loss_AFmax, B_ins_AFmax and B_inv_AFmax (maximum allele frequency of the reported benign genomic regions)
- Add new details in the"AnnotSV_ranking_criteria" output column: (i) detailed scoring points and (ii) remove gene names redundancy
- Add new warnings if the compound heterozygosity analysis is not processed
- Add the "-version" option
- Take into account of a new format in the downloaded OMIM data (approved gene symbol)
- Add bugfix in case of leading or trailing white space in SV type values from the SV input BED file
- Add bugfix in case of no external BED annotation files used
- External BED annotation files can now also be used to report any feature overlapped with the SV (even with 1bp overlap)
- Add bugfix concerning the use of the "-candidateGenesFiltering" option
- Include "NA" in the "-rankFiltering" default option (default = "1-5,NA")
- Add bugfix concerning the use of the "split" annotationMode
- Add bugfix in the SV input BED file, last column could not have empty values. Replaced with "." if empty
- Add bugfix in section 5 of the SV ranking
- Set the ACMG_class to "NA" if not defined
- Update/Add Mouse annotations (CytoBand, miRNA from miRTargetLink)
December 18, 2020, AnnotSV version 3.0
- Major code rewrite and annotations sources reorganization
- Significant modification of the annotations column names
- New SV ranking based on the ACMG guidelines (Riggs et al 2020) as a replacement of the previous ranking (v2.5).
- Add 3 annotation columns: AnnotSV ranking score; ranking decision criteria; AnnotSV ranking class
- Merge pathogenic SV annotation (from multiple sources)
- Pathogenic SV sources: dbVar, ClinGen, ClinVar, OMIM morbid genes
- Add 12 annotation columns:
P_gain_phen; P_gain_hpo; P_gain_source; P_gain_coord;
P_loss_phen; P_loss_hpo; P_loss_source; P_loss_coord;
P_ins_phen; P_ins_hpo; P_ins_source; P_ins_coord;
P_inv_phen; P_inv_hpo; P_inv_source; P_inv_coord
- Remove previous annotation columns from dbVar
- Merge benign SV annotation (from multiple sources)
- Benign SV sources: DGV, ClinVar, ClinGen, DDD, gnomAD, 1000g and IMH
- Add 8 annotation columns:
B_gain_source; B_gain_coord; B_loss_source; B_loss_coord;
B_ins_source; B_ins_coord; B_inv_source; B_inv_coord
- Remove previous annotation columns from DDD, DGV, gnomAD, 1000g and IMH
- Add pathogenic SNV/indel annotation (from ClinVar)
- Add new regulatory elements annotation (EnhancerAtlas)
- Merge regulatory elements annotations into a single column (RefSeq/ENSEMBL, EnhancerAtlas, GeneHancer)
- Update of the annotation data sources with the latest available versions
- The "overlap" option default is now set to 100 % in order to be compliant with the ACMG guidelines
- Add the percent of the CDS overlapped with the SV (in the "split" annotation lines)
- Add the number of overlapped genes in the "full" annotation lines
- By default, AnnotSV now expands the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints (see the "includeCI" option)
November 06, 2020, AnnotSV version 2.5.2
- Add the pLI annotation from gnomAD (pLI_gnomAD), update the pLI annotation from ExAC (pLI_ExAC)
- Add the "LOEUF_bin" annotation (gnomAD)
- Add the "tx start", "tx end" and "Number of exons" annotations
The "tx length" column has been renamed "overlapped tx length"
The "CDS length" column has been renamed "overlapped CDS length"
- If not provided, the EXOMISER_GENE_PHENO_SCORE is set to "-1.0"
- Update README.md
October 13, 2020: AnnotSV version 2.5.1
- fix: Add bugfix when the "SV type" is badly formatted
October 12, 2020: AnnotSV version 2.5
- Add of the "ENCODE blacklist", "Segmental Duplication" and "Gap" annotation datasets
- Fix a critical bug for DGV annotation (GRCh38)
- Add the distance / type to the nearest splice site after considering both breakpoints (distNearestSS and nearestSStype columns)
- Add the in-frame / out-of-frame information from overlapping genes (frameshift column)
- Add decision criteria explaining the ranking (previously available as a separate file)
- Remove of the ranking decision output file (*.ranking.tsv)
- Change the names of the values for the "tx" option:
NM >> RefSeq
ENST >> ENSEMBL
- Add bugfix for exomiser use (don't use some badly formatted NCBI gene ID)
- Add bugfix allowing to use a configfile located in the same directory as the input file
July 30, 2020: AnnotSV version 2.4
- Update of the annotations sources (see the corresponding README section)
- Add of the COSMIC SV dataset (Cancer)
- AnnotSV now reports either RefSeq or Ensembl gene transcripts. Use the new "-tx" option to report either NM or ENST transcripts
=> The « NM » column has been renamed « tx »
=> The “RefGene” directory has been renamed "Genes"
- Add of the "Samples_ID" feature (report of the sample names for which the SV was called)
=> Can be disabled in the AnnotSV configfile
- Include the new "-externalGeneFiles" option to pass external gene file(s) path in the command line
- Integration of 4 Tcl packages (http/tar/csv/json) in the AnnotSV distribution
- Use of the “bcftools” toolset (Li, 2011) to fix a bug with multiallelic sites from VCF input file(s)
=> bcftools is now required if using VCF input file(s)
- Fix the output columns order not being the same depending on the system environment
- "1000g_AF" and "1000g_max_AF" features are not reported anymore
- Add bugfix concerning the CDS length and tx length calculation
- Add bugfix concerning annotation of 2 SV with the same coordinates but from different types (DEL, DUP...)
- Add bugfix with gzipped VCF files as input
- Add bugfix concerning the running of bash scripts (illegal use of | or |& in command)
- Add bugfix concerning the use of the "-snvIndelFiles" and "-candidateSnvIndelSamples" options
- Add bugfix to the Exomiser module
- Add bugfix concerning the AnnotSV installation when PREFIX is not the current directory
- Add bugfix concerning the use of a big "candidateGenesFile"
Dec 20, 2019: AnnotSV version 2.3
- Include phenotype-driven annotations (HPO), based on Exomiser (Smedley et al., 2015)
- Include the lift-over GRCh38 gnomAD SV frequency annotation
- Include the "-annotationsDir" option to pass the annotations directory to AnnotSV at run time
- New "AnnotSV ID" settings (to ensure unique SV identifiers)
- Deletion filtering improvement
- Integration of the gnomAD frequency data in the ranking
- AnnotSV can now create two other output files:
- A report of unannotated variants (e.g. badly formatted SV, variant length < SVminSize...)
- A report of the decisions that explain the ranking of each SV
- Change the names of the misleading following options:
vcfFiles >> snvIndelFiles
vcfPASS >> snvIndelPASS
vcfSamples >> snvIndelSamples
filteredVCFfiles >> candidateSnvIndelFiles
filteredVCFsamples >> candidateSnvIndelSamples
- Annotations are not distributed anymore with the sources but downloaded during the installation with the Makefile
- AnnotSV executable is now directly located in $ANNOTSV/bin to respect the FHS
- Add bugfix concerning the management of BED files
- Add bugfix for the report of the compound heterozygosity (1 SV + 1 SNV/indel)
- Add bugfix concerning the -candidateGenesFiltering option
- Add bugfix concerning the DGV metrics
- Add bugfix concerning the use of the "-sort" Linux command (whose behavior is OS dependant)
- Add bugfix concerning the use of "external gene annotation files"
- Add bugfix concerning the -txFile option
July 09, 2019: AnnotSV version 2.2
- AnnotSV follows now the Filesystem Hierarchy Standard (FHS). Installation can be easily done using a Makefile
- Include 2 new options: "-candidateGenesFiltering" to select the SV overlapping a gene from the "candidateGenesFile" (default = no)
"-rankFiltering" to select the SV of a user-defined specific class (from 1 to 5), default = "1-5"
- Users can now disable default annotation (through a configfile) provided by AnnotSV and only have user defined annotations
- AnnotSV is now available for the Mouse genome SV annotations
- Add the UTR/CDS's information from overlapping genes (location2 column)
- Add bugfix concerning the use of the "-candidateGenesFile" and "-reciprocal" options
- Add bugfix concerning the report of the SV length
- Add bugfix concerning the report of gene-based annotation on the full lines
Apr 18, 2019: AnnotSV version 2.1
- Include the gnomAD SV frequency annotation
- Include the Ira M. Hall’s lab SV frequency annotations
- Include GeneHancer annotation (an integrated compendium of human promoters, enhancers and their inferred target genes)
WARNING: not supplied as part of the AnnotSV sources. Users need to request the up-to-date GeneHancer data dedicated to AnnotSV
- Include 2 new options: "-overwrite" to overwrite existing output results (default = yes)
"-txFile" to specify a list of preferred genes transcripts to be used in priority during the annotation
- Default of the -SVinputInfo option is now set to 1 (the additional fields from the SV input file are reported in the outputfile)
- Large bed annotation files are presorted, in order to be compatible for server with low specifications
- Improve error messages and exit management (return a non-zero exit code in case of error or zero if all went fine)
- AnnotSV minimum requirement is now starting with Tcl 8.5
- Add bugfix concerning the homozygous and heterozygous SNV/indel counts within the SV to annotate
- Add bugfix for the SV ranking (when the -metrics option was set to "fr")
- Add bugfix concerning the "-reciprocal" option
Dec 21, 2018: AnnotSV version 2.0
- Add ranking/classification for SV in 5 classes (from benign to pathogenic)
- Include 12 additional annotations including:
-> the creation of a unique identifier for each SV
-> the SV length
-> the SV type (DEL, DUP, ...)
-> the SV ranking/classification
-> the OMIM morbid genes
-> the ClinGen Haploinsufficiency Score
-> the ClinGen Triplosensitivity Score
-> the ACMG genes
-> the CNV intolerance from ExAC
- Add of the "metrics" option to change numerical values to us or fr metrics (e.g. 0.2 or 0,2)
- Add bugfix concerning empty SV input file: return a non-zero exit status (1) to continue processing in a pipeline
- Modification of the directories structure for the annotation. Please look at the README file.
- Options: "SVfromDBoverlap", "FeaturesOverlap" and "SVtoAnnOverlap" have been replaced by "reciprocal" and "overlap"
- By default, AnnotSV now reports the additional fields from the SV BED input file
- Report of the input BED file header in the output
- Update of all annotation sources provided with AnnotSV
Sep 28, 2018: AnnotSV version 1.2
- Support the integration of user defined annotated regions imported from BED and/or TSV file(s) into the output file
- Include 3 additional annotations based on the dbVar pathogenic NR SV dataset:
-> The dbVar NR SV event types (e.g. deletion, duplication…)
-> The dbVar NR SV accession (e.g. nssv1415016)
-> The dbVar NR SV clinical assertion (e.g. pathogenic, likely pathogenic)
- Include 1 new option (-typeOfAnnotation) to configure the types of lines produced by AnnotSV (both, full or split)
- OutputFile extension will always be a “.tsv” (tab separated values) extension
- Add bugfix concerning large SV and TAD boundaries annotation
May 16, 2018: AnnotSV version 1.1.1
- Add bugfix concerning 1000g annotation (in some cases, an insertion could be not reported and AnnotSV stopped working properly)
Mar 20, 2018: AnnotSV version 1.1
- Add bugfix concerning counts of the homozygous and heterozygous variants in VCF files
- Support for new SV input file format: VCF file (4.3) can now be used to describe the SV to annotate (in addition to the BED format)
The "-bedFile" option has now been renamed "-SVinputFile"
The "-bedInfo" option has now been renamed "-SVinputInfo". Default is now set to 0 (the additional fields from the SV input file are not reported in the outputfile)
- Report additional information while counting variants in the SNV/indel input file(s):
-> The number of SNV/indel loaded
-> The number of SNV/indel not considered because of the “FILTER” column value
-> The number of SNV/indel not considered because of the absence of genotype information (“GT” value can be absent in bad VCF formatted files)
-> The number of SV present but not considered for that purpose (only SNV/indel are taken into account)
- Set the default value of the -vcfPASS option to 0 (to be non-restrictive and consider all variants in the VCF by default).
- Include 2 new options (-outputDir and -outputFile) to specify the output directory and file name
- Include 3 additional annotations based on the 1000 genomes phase 3 dataset:
-> The type of event (i.e. DEL, ALU, DUP, <CN3>...)
-> The global allele frequency
-> The maximum observed allele frequency across populations
- Include a new option (-SVminSize) to set the SV minimum size (in bp). Default is 50 (bp)
Dec 21, 2017: AnnotSV version 1.0
================================================
FILE: commandLineOptions.txt
================================================
COMMAND LINE USAGE
$ANNOTSV/bin/AnnotSV -SVinputFile 'Path of your VCF or BED input file with SV coordinates' >& AnnotSV.log &
OPTIONS
-annotationsDir: Path of the annotations directory
-annotationMode: Description of the types of lines produced by AnnotSV
Values: both (default), full or split
-bcftools: Path of the bcftools local installation
-bedtools: Path of the bedtools local installation
-benignAF: Allele frequency threshold to select the benign SV in the data sources
Range values: [0.001-0.1], default = 0.01 (i.e. 1%)
-bracketedAltMaxSize: Maximum SV length (Mb) for SVTYPE inference from bracketed ALT values
Values: positive float (default: 10; above 10 Mb, bracketed ALT is treated as BND)
-bracketedAltMode: Defines how bracketed ALT values in VCF are interpreted:
The SV can be considered as DEL, DUP, INS or INV, or considered as BND (TRA is always reported as BND)
Values: ALL (default, infer all compatible SVTYPE: DEL,DUP,INS,INV)
BND (treat all bracketed ALT as BND)
comma-separated SVTYPE values among DEL, DUP, INS or INV (infer only selected SVTYPE; e.g.: "DEL,DUP". Others are treated as BND)
-breakpointProximity: Maximum allowed distance (bp) between SV and feature breakpoints (start-to-start and end-to-end).
Values: positive int (default: 100)
-candidateGenesFile: Path of a file containing the candidate genes of the user (gene names can be space-separated, tabulation-separated, or line-break-separated)
-candidateGenesFiltering: To select only the SV annotations ("split" and "full") overlapping a gene from the "candidateGenesFile"
Values: 0 (default) or 1
-candidateSnvIndelFiles: Path of the filtered VCF input file(s) with SNV/indel coordinates for compound heterozygotes report (optional)
Gzipped VCF files are supported as well as regular expression
-candidateSnvIndelSamples: To specifiy the sample names from the VCF files defined with the -candidateSnvIndelFiles option (sample names can be coma-separated or semicolon -separated)
Default: use all samples from the filtered VCF files
-genomeBuild: Genome build used
Values: GRCh38 (default) or GRCh37 or CHM13 or or mm9 or mm10
-help: More information on the arguments
-hpo: HPO terms list describing the phenotype of the individual being investigated
Values: use comma, semicolon or space separated class values
Default = "" (e.g.: "HP:0001156,HP:0001363,HP:0011304")
-includeCI: To expand the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints
AnnotSV keeps the CIPOS and CIEND information that comes first in the INFO column (even if the fields are CIPOS95, CIEND95 or tool_CIPOS, tool_CIEND).
Values: 1 (default) or 0
-metrics: Changing numerical values from frequencies to us or fr metrics (e.g. 0.2 or 0,2)
Values: us (default) or fr
-minTotalNumber: Minimum number of individuals tested to consider a benign SV for the ranking
Range values: [100-1000], default = 500
-missingGTinSamplesid: To report sample IDs with missing alleles in the GT field (./. or .|.) in the "Samples_ID" output field
Values: 1 (default) or 0
-outputDir: Output path name
-outputFile: Output path and file name
-overlap: Minimum overlap (%) between user features (User BED) and the annotated SV to be reported
Range values: [0-100], default = 100
-overwrite: To overwrite existing output results
Values: 1 (default) or 0
-promoterSize: Number of bases upstream from the transcription start site
Default = 500
-rankFiltering: To select the SV of a user-defined specific class (from 1 to 5; or NA)
Values: use comma separated class values, or use a dash to denote a range of values
(e.g.: "3,4,5" or "3-5"), default = "1-5,NA"
-reciprocal: Use of a reciprocal overlap between SV and user features (only for annotations with features overlapping the SV)
Values: 0 (default) or 1
-REreport: Create a report to link the annotated SV and the overlapped regulatory elements (coordinates and sources)
Values: 0 (default) or 1
-REselect1: To report only the morbid, HI, TS, candidate and phenotype matched genes
Values: 1 (default) or 0
-REselect2: To report only the genes not present in "Gene_name"
Values: 1 (default) or 0
-samplesidBEDcol: Number of the column reporting the samples ID for which the SV was called (if the input SV file is a BED)
Range values: [4-[, default = -1 (value not given)
(Samples ID should be comma or space separated)
-snvIndelFiles: Path of the VCF input file(s) with SNV/indel coordinates used for false positive discovery
Use counts of the homozygous and heterozygous variants
Gzipped VCF files are supported as well as regular expression
-snvIndelPASS: Boolean. To only use variants from VCF input files that passed all filters during the calling (FILTER column value equal to PASS)
Values: 0 (default) or 1
-snvIndelSamples: To specify the sample names from the VCF files defined from the -snvIndelFiles option
Default: use all samples from the VCF files
-SVinputFile: Path of the input file (VCF or BED) with SV coordinates
Gzipped VCF file is supported
-SVinputInfo: To extract the additional SV input fields and insert the data in the outputfile
Values: 1 (default) or 0
-SVminSize: SV minimum size (in bp)
AnnotSV does not annotate small deletion, insertion and duplication from a VCF input file
Default = 50
-svtBEDcol: Number of the column describing the SV type (DEL, DUP) if the input SV file is a BED
Range values: [4-[, default = -1 (value not given)
-tx: Origin of the transcripts (RefSeq or ENSEMBL)
Values: RefSeq (default) or ENSEMBL
-txFile: Path of a file containing a list of preferred genes transcripts to be used in priority during the annotation (Preferred genes transcripts names should be tab or space separated)
-variantconvertDir: Path of the variantconvert directory
(by default, the variantconvert tool distributed by annotSV is used)
-variantconvertMode: variantconvert conversion mode
Values: combined (default) or full or fullsplit
-version: Version of the AnnotSV program
-vcf: Creation of a VCF output file format (-svtBEDcol needs to be defined too)
Values: 0 (default) or 1
================================================
FILE: etc/AnnotSV/application.properties
================================================
#
# The Exomiser - A tool to annotate and prioritize genomic variants
#
# Copyright (c) 2016-2018 Queen Mary University of London.
# Copyright (c) 2012-2016 Charit Universittsmedizin Berlin and Genome Research Ltd.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
spring.application.name=exomiser-prioritiser-service
server.servlet.context-path=/exomiser/api/prioritise
server.port=XXXX
server.servlet.application-display-name=Exomiser Prioritiser Server
#Absolute system path where the exomiser data is installed
#exomiser.data-directory=${project.build.testOutputDirectory}
exomiser.data-directory=YYYY
exomiser.phenotype.data-version=ZZZZ
exomiser.phenotype.random-walk-preload=true
#Actuator configuration
info.name=${server.display-name}
info.build.version=${project.version}
info.build.timestamp=${build.timestamp}
================================================
FILE: etc/AnnotSV/configfile
================================================
# This file is used to simplify the configuration of AnnotSV.
# Anything behind a hashtag is considered as a comment
# Please, feel free to change the AnnotSV options.
#------------------
# AnnotSV Options :
#------------------
-annotationMode: "both"
-benignAF: 0.01
-candidateGenesFiltering: 0
-genomeBuild: "GRCh38"
-hpo: ""
-includeCI: 1
-metrics: "us"
-minTotalNumber: "500"
-overlap: 100
-overwrite: 1
-promoterSize: 500
-rankFiltering: "1-5,NA"
-reciprocal: 0
-snvindelPASS: 0
-SVinputInfo: 1
-SVminSize: 50
-variantconvertMode: "combined"
-vcf: 0
#------------------------
# AnnotSV Output columns:
#------------------------
# Output column names are listed below.
# In order to disable default annotations provided by AnnotSV, some column names (the ones that are not marked with an *) can be commented with a hash character ("#") by the user.
AnnotSV_ID *
SV_chrom *
SV_start *
SV_end *
SV_length *
SV_type *
Samples_ID *
Annotation_mode *
# Genes annotations:
CytoBand
Gene_name *
Closest_left
Closest_right
Gene_count *
Tx *
Tx_version
Tx_start *
Tx_end *
Overlapped_tx_length *
Overlapped_CDS_length *
Overlapped_CDS_percent *
Frameshift *
Exon_count *
Location *
Location2 *
Dist_nearest_SS *
Nearest_SS_type *
Intersect_start *
Intersect_end *
# Regulatory Elements annotations:
RE_gene *
# Annotations with benign genes or genomic regions:
B_gain_source *
B_gain_coord *
B_gain_AFmax *
B_loss_source *
B_loss_coord *
B_loss_AFmax *
B_ins_source
B_ins_coord
B_ins_AFmax
B_inv_source
B_inv_coord
B_inv_AFmax
po_B_gain_allG_source *
po_B_gain_allG_coord *
po_B_gain_someG_source *
po_B_gain_someG_coord *
po_B_loss_allG_source *
po_B_loss_allG_coord *
po_B_loss_someG_source *
po_B_loss_someG_coord *
# Annotations with pathogenic genes or genomic regions:
P_gain_phen *
P_gain_hpo *
P_gain_source *
P_gain_coord *
P_loss_phen *
P_loss_hpo *
P_loss_source *
P_loss_coord *
P_ins_phen
P_ins_hpo
P_ins_source
P_ins_coord
P_inv_phen
P_inv_hpo
P_inv_source
P_inv_coord
po_P_gain_phen *
po_P_gain_hpo *
po_P_gain_source *
po_P_gain_coord *
po_P_gain_percent *
po_P_loss_phen *
po_P_loss_hpo *
po_P_loss_source *
po_P_loss_coord *
po_P_loss_percent *
# Annotations with pathogenic snv/indel:
P_snvindel_nb *
P_snvindel_phen *
# Cancer
Cosmic_ID *
Cosmic_mut_typ *
# Breakpoints annotations
TAD_coordinate
ENCODE_experiment
GC_content_left
GC_content_right
Repeat_coord_left
Repeat_type_left
Repeat_coord_right
Repeat_type_right
Gap_left
Gap_right
SegDup_left
SegDup_right
ENCODE_blacklist_left
ENCODE_blacklist_characteristics_left
ENCODE_blacklist_right
ENCODE_blacklist_characteristics_right
# Gene-based annotations:
ACMG
HI *
TS *
GenCC_disease
GenCC_moi
GenCC_classification
GenCC_pmid
NCBI_gene_ID
HGNC_gene_ID
DDD_status
DDD_mode
DDD_consequence
DDD_disease
DDD_pmid
DDD_HI_percent *
ExAC_synZ
ExAC_misZ
ExAC_delZ
ExAC_dupZ
ExAC_cnvZ
LOEUF_bin *
ExAC_pLI
GnomAD_pLI *
OMIM_morbid *
OMIM_morbid_candidate
OMIM_ID
OMIM_phenotype
OMIM_inheritance
GnomAD_pLI *
PhenoGenius_score
PhenoGenius_phenotype
PhenoGenius_specificity *
Exomiser_gene_pheno_scorea *
Human_pheno_evidence
Mouse_pheno_evidence
Fish_pheno_evidence
# Ranking:
AnnotSV_ranking_score *
AnnotSV_ranking_criteria *
ACMG_class *
#--------------------------
# AnnotSV ranking criteria:
#--------------------------
# The comprehensive and detailed scoring guidelines are available at:
# https://lbgi.fr/AnnotSV/Documentation/Scoring_Criteria_AnnotSV_latest.xlsx
# Customizing the weights of AnnotSV ranking criteria
# ---------------------------------------------------
# To adjust the importance of each criterion in the AnnotSV ranking,
# modify the values below. Values can be positive or negative floats.
# Loss
1A_Loss 0.00
1B_Loss -0.60
2A_Loss 1.00
2B_Loss 0.00
2C-1_Loss 0.90
2C-2_Loss 0.00
2D-1_Loss 0.00
2D-2_Loss 0.90
2D-3_Loss 0.45
2D-4_Loss 0.90
2E-1_Loss 0.90
2E-2_Loss 0.45
2E-3_Loss 0.30
2E-4_Loss 0.20
2F-4O_Loss -1.00
2G_Loss 0.00
2H_Loss 0.15
3A_Loss 0.00
3B_Loss 0.45
3C_Loss 0.90
4O_Loss -1.00
5F_Loss 0.00
5G_Loss 0.10
5H_Loss 0.30
# Gain
1A_Gain 0.00
1B_Gain -0.60
2A_Gain 1.00
2B_Gain 0.00
2C_Gain -1.00
2D_Gain -1.00
2E_Gain 0.00
2F_Gain -1.00
2G_Gain 0.00
2H-1_Gain 0.45
2H-2_Gain 0.00
2I-1_Gain 0.45
2I-2_Gain 0.45
2I-3_Gain 0.00
2J_Gain 0.00
2K_Gain 0.45
2L_Gain 0.00
3A_Gain 0.00
3B_Gain 0.45
3C_Gain 0.90
4O_Gain 0.00
5F_Gain 0.00
5G_Gain 0.10
5H_Gain 0.15
================================================
FILE: share/bash/AnnotSV/checkPhenoGeniusCliInstall.sh
================================================
#!/bin/bash
# Bash script:
# A successfully executed code should exit with code 0.
# Other values indicate an error.
# Poetry is required
####################
poetryDir=`which poetry`
# The "$poetryDir" directory should exist
if [ ! -e "$poetryDir" ]
then
echo "Poetry seems not to be installed"
echo "WARNING: No PhenoGenius annotations available."
exit 1
fi
# Poetry version
################
# poetryVersion=`poetry --version | sed "s/Poetry (version //" | sed "s/)//"`
# e.g. Poetry (version 1.5.1)
# echo "Poetry: $poetryVersion"
# PhenogeniusCli install (if needed)
####################################
mkdir -p $ANNOTSV/share/python3/phenogeniuscli
cd $ANNOTSV/share/python3/phenogeniuscli
if [ ! -d PhenoGeniusCli ]
then
git clone https://github.com/kyauy/PhenoGeniusCli.git >> PhenoGeniusCli.install.log 2>&1
cd ./PhenoGeniusCli >> PhenoGeniusCli.install.log 2>&1
# Search for the last PhenoGenius version tested/validated with AnnotSV
git checkout tags/v.1.1.3 >> ../PhenoGeniusCli.install.log 2>&1
rm -rf .git .gitattributes .github .gitignore >> ../PhenoGeniusCli.install.log 2>&1
poetry config keyring.enabled false
poetry install &> ../poetry_install.log
fi
cd $ANNOTSV/share/python3/phenogeniuscli/PhenoGeniusCli
poetry run python3 phenogenius_cli.py --help &> ../PhenoGenius.run.test1.log
if [ `grep -c -- "--hpo_list" ../PhenoGenius.run.test1.log` == "1" ]
then
exit 0
else
poetry config keyring.enabled false
poetry install &> ../poetry_install.log ;# Can be run from different servers
poetry run python3 phenogenius_cli.py --help &> ../PhenoGenius.run.test2.log
if [ `grep -c -- "--hpo_list" ../PhenoGenius.run.test2.log` == 1 ]
then
exit 0
else
echo "phenogenius_cli.py not installed"
echo "WARNING: No PhenoGenius annotations available."
exit 1
fi
fi
================================================
FILE: share/bash/AnnotSV/searchForAFreePortNumber.bash
================================================
#!/bin/bash
# com: Compare two sorted files line by line. Output the lines that are common, plus the lines that are unique.
# comm [options]... File1 File2
# -2 Suppress lines unique to file2
# -3 Suppress lines that appear in both files
#
# seq: print a sorted sequence of numbers from 5000 to 50000
#
# ss: used to dump socket statistics.
# -H, --no-header
# -n, --numeric
# Do not try to resolve service names. Show exact bandwidth
# values, instead of human-readable.
# -t, --tcp
# Display TCP sockets.
# e.g. "ss -Htan" >>> "LISTEN 0 5 0.0.0.0:63864 0.0.0.0:*"
comm -23 <(seq 5000 50000 | sort) <(ss -Htan | awk '{print $4}' | cut -d':' -f2 | sort -u) | head -n 1
================================================
FILE: share/doc/AnnotSV/Example/README.commands
================================================
$ANNOTSV/bin/AnnotSV -SVinputFile test1.bed -outputFile ./test1.annotated.tsv -svtBEDcol 4 -genomeBuild GRCh37 -vcf 1
$ANNOTSV/bin/AnnotSV -SVinputFile test2.vcf -outputFile ./test2.annotated.tsv -genomeBuild GRCh37 -vcf 1
================================================
FILE: share/doc/AnnotSV/Example/test1.annotated.tsv
================================================
AnnotSV_ID SV_chrom SV_start SV_end SV_length SV_type Biologist_annotation Biologist_ranking Samples_ID Annotation_mode CytoBand Gene_name Closest_left Closest_right Gene_count Tx Tx_version Tx_start Tx_end Overlapped_tx_length Overlapped_CDS_length Overlapped_CDS_percent Frameshift Exon_count Location Location2 Dist_nearest_SS Nearest_SS_type Intersect_start Intersect_end RE_gene P_gain_phen P_gain_hpo P_gain_source P_gain_coord P_loss_phen P_loss_hpo P_loss_source P_loss_coord P_ins_phen P_ins_hpo P_ins_source P_ins_coord po_P_gain_phen po_P_gain_hpo po_P_gain_source po_P_gain_coord po_P_gain_percent po_P_loss_phen po_P_loss_hpo po_P_loss_source po_P_loss_coord po_P_loss_percent P_snvindel_nb P_snvindel_phen B_gain_source B_gain_coord B_gain_AFmax B_loss_source B_loss_coord B_loss_AFmax B_ins_source B_ins_coord B_ins_AFmax B_inv_source B_inv_coord B_inv_AFmax po_B_gain_allG_source po_B_gain_allG_coord po_B_gain_someG_source po_B_gain_someG_coord po_B_loss_allG_source po_B_loss_allG_coord po_B_loss_someG_source po_B_loss_someG_coord GC_content_left GC_content_right Repeat_coord_left Repeat_type_left Repeat_coord_right Repeat_type_right Gap_left Gap_right SegDup_left SegDup_right ENCODE_blacklist_left ENCODE_blacklist_characteristics_left ENCODE_blacklist_right ENCODE_blacklist_characteristics_right ACMG HI TS DDD_HI_percent ExAC_delZ ExAC_dupZ ExAC_cnvZ ExAC_synZ ExAC_misZ GenCC_disease GenCC_moi GenCC_classification GenCC_pmid NCBI_gene_ID HGNC_gene_ID OMIM_ID OMIM_phenotype OMIM_inheritance OMIM_morbid OMIM_morbid_candidate LOEUF_bin GnomAD_pLI ExAC_pLI AnnotSV_ranking_score AnnotSV_ranking_criteria ACMG_class
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA full q11.21 DGCR6;PRODH;LOC122455341;DGCR5;FAM246C;DGCR2;DGCR11;ESS2;TSSK2;GSC2;LINC01311;SLC25A1;CLTCL1;HIRA;MRPL40;C22orf39;UFD1-AS1;UFD1;CDC45;CLDN5;LINC00895;SEPTIN5;SEPT5-GP1BB;GP1BB;TBX1;GNB1L;RTL10;TXNRD2;COMT;MIR4761;ARVCF;TANGO2;MIR185;DGCR8;MIR3618;MIR1306;TRMT2A;MIR6816;RANBP1;SNORA77B;ZDHHC8;CCDC188;LINC02891;LINC00896;RTN4R;MIR1286;DGCR6L;FAM230A;FAM247B;GGTLC3;TMEM191B;PI4KAP1;RIMBP3;FAM246B;FAM230J;FAM230G;ZNF74;SCARF2;KLHL22;MED15;POM121L4P;TMEM191A;PI4KA;SERPIND1;SNAP29;CRKL;LINC01637;AIFM3;LZTR1;THAP7;THAP7-AS1;TUBA3FP;P2RX6;SLC7A4;MIR649;P2RX6P;LRRC74B;BCRP2 FAM230F LOC102724728 78 ABL1 (morbid/RE=mTL_miRNA);ACTN4 (morbid/RE=mTL_miRNA);ACVR2B (morbid/RE=mTL_miRNA);ADA2 (morbid/RE=ABC_enhancer);ADAR (morbid/RE=mTL_miRNA);ADH5 (morbid/RE=mTL_miRNA);AFF2 (HI=3/morbid/RE=mTL_miRNA);AGO1 (morbid/RE=mTL_miRNA);AGO2 (morbid/RE=mTL_miRNA);AHI1 (morbid/RE=mTL_miRNA);AHR (morbid/RE=mTL_miRNA);AKT1 (morbid/RE=mTL_miRNA);ALG1 (morbid/RE=mTL_miRNA);AMH (morbid/RE=mTL_miRNA);APCDD1 (morbid/RE=mTL_miRNA);AR (HI=3/morbid/RE=mTL_miRNA);ARID1A (HI=3/morbid/RE=mTL_miRNA);ASH1L (HI=3/morbid/RE=mTL_miRNA);ATM (HI=3/morbid/RE=mTL_miRNA);ATP6AP1 (morbid/RE=mTL_miRNA);ATP6V0A2 (morbid/RE=mTL_miRNA);ATP6V1E1 (morbid/RE=ABC_enhancer);ATR (morbid/RE=mTL_miRNA);B4GALT1 (morbid/RE=mTL_miRNA);BACH1 (morbid/RE=mTL_miRNA);BAP1 (HI=3/morbid/RE=mTL_miRNA);BBS5 (morbid/RE=mTL_miRNA);BCL10 (morbid/RE=mTL_miRNA);BLOC1S6 (morbid/RE=mTL_miRNA);BMPR1A (HI=3/morbid/RE=mTL_miRNA);BNC2 (morbid/RE=mTL_miRNA);BRD4 (morbid/RE=mTL_miRNA);C3 (morbid/RE=mTL_miRNA);CACNA1C (morbid/RE=mTL_miRNA);CAD (morbid/RE=mTL_miRNA);CALM3 (morbid/RE=mTL_miRNA);CAPN15 (morbid/RE=mTL_miRNA);CAPNS1 (morbid/RE=mTL_miRNA);CASP14 (morbid/RE=mTL_miRNA);CBL (morbid/RE=mTL_miRNA);CCDC134 (morbid/RE=mTL_miRNA);CCDC88A (morbid/RE=mTL_miRNA);CCND2 (morbid/RE=mTL_miRNA);CCNQ (morbid/RE=mTL_miRNA);CDC42 (morbid/RE=mTL_miRNA);CEP104 (morbid/RE=mTL_miRNA);CERS1 (morbid/RE=mTL_miRNA);CHRDL1 (HI=3/morbid/RE=mTL_miRNA);CLCC1 (morbid/RE=mTL_miRNA);CLCN7 (morbid/RE=mTL_miRNA)... 22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1);Schwannomatosis CLN:906110;CLN:906111;CLN:917324;TS3:ISCA-37433;dbVar:nssv15121202;dbVar:nssv15132168;dbVar:nssv15132429;dbVar:nssv15132430;dbVar:nssv15132553;dbVar:nssv15132642;nssv15139997;dbVar:nssv15132749;dbVar:nssv15133139;dbVar:nssv15133442;dbVar:nssv15133527;dbVar:nssv15133528;dbVar:nssv15133531;dbVar:nssv15133921;dbVar:nssv15134211;dbVar:nssv15134239;dbVar:nssv15134353;dbVar:nssv15136015;dbVar:nssv15137439;dbVar:nssv15138177;dbVar:nssv15138869;dbVar:nssv15140282;dbVar:nssv15141369;dbVar:nssv15153269;dbVar:nssv15156361;dbVar:nssv15605811;dbVar:nssv15605831;dbVar:nssv15605876;dbVar:nssv15755816;dbVar:nssv16207465;dbVar:nssv16736612;dbVar:nssv16736616;dbVar:nssv18830899;dbVar:nssv18830992 22:18894836-20311784;22:18894836-21461752;22:18894836-21464119;22:18896973-21440514;22:18900756-21075586;22:18908833-21358123;22:18909039-21440514;22:18909045-21464119;22:18912232-20287208;22:18912515-21431174;22:18916828-21050078;22:18916829-20312661;22:18916843-20311810;22:18916843-20311858;22:18916843-20312661;22:18919943-20311763;22:18919943-20659606;22:18919943-20708934;22:18919943-21440514;22:18923899-21431174;22:18937381-21459713;22:18938162-21455556;22:18950767-21455556;22:18970562-21040836;22:18973253-21435405;22:19168759-20942862;22:20895156-21374512;22:20958985-21379958;22:21044197-21440455;22:21045039-21455556;22:21065883-21440455;22:21081261-21440455;22:21086707-21445960;22:21300291-21331188;22:21344737-21344807;22:21345949-21346047;22:21348439-21348534 22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1);Bernard-Soulier syndrome, type B, 231200 (3) AR;Giant platelet disorder, isolated, 231200 (3) AR;Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome, 609528 (3) AR;Combined D-2- and L-2-hydroxyglutaric aciduria, 615182 (3) AR;Myasthenic syndrome, congenital, 23, presynaptic, 618197 (3) AR;Conotruncal anomaly face syndrome, 217095 (3);DiGeorge syndrome, 188400 (3) AD;Tetralogy of Fallot, 187500 (3) AD;Velocardiofacial syndrome, 192430 (3) AD;DiGeorge_syndrome;Gastrointestinal defects and immunodeficiency syndrome 2, 619708 (3) AR;Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, 616531 (3) AR;Spastic paraplegia 84, AR, 619621 (3) AR;Hyperprolinemia, type I, 239500 (3) AR;Schizophrenia, susceptibility to, 4, 600850 (3) AD;Meier-Gorlin syndrome 7, 617063 (3) AR;Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration, 616878 (3) AR;Noonan syndrome 10, 616564 (3) AD;Noonan syndrome 2, 605275 (3) AR;Schwannomatosis-2, susceptibility to, 615670 (3) AD;Recurrent_metabolic_encephalomyopathic_crises-rhabdomyolysis-cardiac_arrhythmia-intellectual_disability_syndrome|Intellectual_disability|Acute_rhabdomyolysis|Episodic_flaccid_weakness|Seizure|Cardiac_arrhythmia;Thrombophilia 10 due to heparin cofactor II deficiency, 612356 (3) AD;Van den Ende-Gupta syndrome, 600920 (3) AR HP:0000730;HP:0001249;HP:0001250;HP:0001267;HP:0001275;HP:0001286;HP:0001303;HP:0001656;HP:0001661;HP:0001665;HP:0001666;HP:0001687;HP:0001721;HP:0002122;HP:0002125;HP:0002182;HP:0002192;HP:0002279;HP:0002306;HP:0002316;HP:0002348;HP:0002382;HP:0002386;HP:0002391;HP:0002402;HP:0002417;HP:0002430;HP:0002431;HP:0002432;HP:0002434;HP:0002437;HP:0002458;HP:0002466;HP:0002479;HP:0002482;HP:0002499;HP:0002543;HP:0002794;HP:0003752;HP:0003767;HP:0004351;HP:0005158;HP:0006833;HP:0006997;HP:0007154;HP:0007176;HP:0007180;HP:0008942;HP:0010520;HP:0011675 CLN:226591;CLN:2871255;CLN:959024;HI3:ISCA-37433;dbVar:nssv15119864;dbVar:nssv15120710;dbVar:nssv15124351;dbVar:nssv15124515;dbVar:nssv15129189;dbVar:nssv15130834;dbVar:nssv15130929;dbVar:nssv15131088;dbVar:nssv15131611;dbVar:nssv15132323;nssv15139981;dbVar:nssv15132334;dbVar:nssv15132747;dbVar:nssv15132748;dbVar:nssv15132933;dbVar:nssv15132934;dbVar:nssv15132935;dbVar:nssv15132939;dbVar:nssv15133099;dbVar:nssv15133185;dbVar:nssv15133186;dbVar:nssv15133443;dbVar:nssv15133817;dbVar:nssv15134350;nssv15139984;dbVar:nssv15134354;dbVar:nssv15134360;dbVar:nssv15134361;dbVar:nssv15134635;dbVar:nssv15134703;dbVar:nssv15134820;dbVar:nssv15134849;dbVar:nssv15136233;dbVar:nssv15137726;dbVar:nssv15137759;dbVar:nssv15137802;dbVar:nssv15138106;dbVar:nssv15138475;dbVar:nssv15139405;dbVar:nssv15139434;dbVar:nssv15139445;nssv15774763;dbVar:nssv15139759;dbVar:nssv15140043;dbVar:nssv15140048;dbVar:nssv15140057;dbVar:nssv15141198;dbVar:nssv15141722;dbVar:nssv15142496;dbVar:nssv15143197;dbVar:nssv15143645;dbVar:nssv15144279;dbVar:nssv15144449;dbVar:nssv15153165;dbVar:nssv15154011;dbVar:nssv15155693;dbVar:nssv15156360;dbVar:nssv15162020;dbVar:nssv15162021;dbVar:nssv15605807;dbVar:nssv15605829;dbVar:nssv15605830;nssv16216546;dbVar:nssv15605834;dbVar:nssv15755310;dbVar:nssv15755712;dbVar:nssv15755812;dbVar:nssv15770037;dbVar:nssv15770783;dbVar:nssv15770877;dbVar:nssv15772938;nssv15773614;nssv15775115;nssv15775184;nssv15775592;dbVar:nssv15772982;dbVar:nssv15775129;dbVar:nssv15776509;dbVar:nssv15776863;dbVar:nssv15776865;dbVar:nssv15776871;dbVar:nssv16208595;dbVar:nssv16208596;dbVar:nssv16212111;dbVar:nssv16213307;dbVar:nssv16213808;dbVar:nssv16214784;dbVar:nssv16215255;dbVar:nssv16215257;dbVar:nssv16216543;dbVar:nssv16216544;nssv8639845;nssv15161831;dbVar:nssv16254574;dbVar:nssv16254739;dbVar:nssv16255831;dbVar:nssv16736634;dbVar:nssv17171460;nssv17974163;dbVar:nssv17171461;dbVar:nssv17171462;dbVar:nssv17171559;dbVar:nssv17171582;dbVar:nssv17171772;dbVar:nssv17649936;dbVar:nssv17649973;dbVar:nssv17955605;dbVar:nssv17955606;dbVar:nssv17955868;dbVar:nssv17970829;dbVar:nssv17971092;dbVar:nssv17971094;dbVar:nssv17971356;dbVar:nssv17971399;dbVar:nssv17977042;dbVar:nssv18329601;dbVar:nssv18329824;dbVar:nssv18330264;dbVar:nssv18330322;dbVar:nssv18330820;dbVar:nssv18786380;dbVar:nssv18790095;dbVar:nssv18792883;dbVar:nssv18841927;nssv18830898;dbVar:nssv8639589;nssv15122532;morbid:CDC45;morbid:GP1BB;morbid:LZTR1;morbid:PI4KA;morbid:PRODH;morbid:SCARF2;morbid:SERPIND1;morbid:SLC25A1;morbid:SNAP29;morbid:TANGO2;morbid:TBX1 22:18894836-20238206;22:18894836-20311763;22:18894836-20659606;22:18894836-21440514;22:18894836-21461752;22:18894836-21461811;22:18894836-21464119;22:18896973-20311763;22:18896973-21382953;22:18896973-21440514;22:18899288-18925066;22:18900294-18924066;22:18900295-18923806;22:18900443-21440514;22:18900669-18923820;22:18900669-19747220;22:18900669-19770565;22:18900689-21351637;22:18900896-18923882;22:18901005-21408430;22:18905110-19015451;22:18910311-18923800;22:18910311-18923820;22:18910311-19770565;22:18912232-20287208;22:18912404-21431174;22:18912871-21431174;22:18915348-21463730;22:18916828-20311858;22:18916829-20312661;22:18916829-21041014;22:18916829-21049800;22:18916843-19004772;22:18916843-20310938;22:18916843-20311858;22:18916843-20312661;22:18916843-20716903;22:18916843-20767095;22:18916843-21011216;22:18916843-21033371;22:18916843-21075592;22:18916844-20311858;22:18916844-21033401;22:18916844-21075592;22:18918742-20311922;22:18919580-21460595;22:18919943-20311763;22:18919943-20659606;22:18919943-20708934;22:18919943-21025713;22:18919943-21440514;22:18922152-21449911;22:18938162-20229017;22:18938162-20996250;22:18938162-21455556;22:18962314-21455556;22:18973253-21435405;22:18999804-21455499;22:18999804-21455556;22:19016664-21463730;22:19023802-21440455;22:19023802-21440514;22:19035018-21461811;22:19035324-21464119;22:19036287-21208284;22:19058830-21440514;22:19156118-19529130;22:19163094-19166249;22:19163624-19770565;22:19184001-21416024;22:19336599-21208828;22:19467443-19508131;22:19470352-19481849;22:19647906-21153690;22:19709401-21142058;22:19709436-19712313;22:19709952-19963280;22:19710419-21142058;22:19711062-19712294;22:19711829-19711877;22:19743227-19755855;22:19743425-19747210;22:19743425-19754400;22:19743425-19770565;22:19743474-19747220;22:19747168-19754390;22:19748301-19754857;22:19748451-19748647;22:20008633-20054687;22:20027161-20063237;22:20028564-20053554;22:20028990-20062723;22:20028993-20062955;22:20029136-20062954;22:20029701-20062756;22:20030823-20041691;22:20030823-20053554;22:20030859-20052185;22:20030879-20049206;22:20030879-20052185;22:20036383-20045782;22:20036384-20045781;22:20036385-20045784;22:20039969-20043556;22:20708891-21407690;22:20718171-21427936;22:20733496-21463730;22:20745763-21460658;22:20754408-21440515;22:20754408-21457610;22:20754423-21461752;22:20778874-20792112;22:20921343-21459713;22:21061979-21213099;22:21062169-21463730;22:21062567-21463730;22:21065883-21455556;22:21067570-21414817;22:21069074-21463730;22:21074921-21440514;22:21075576-21454721;22:21081285-21457610;22:21128401-21142008;22:21213295-21245502;22:21335907-21346541;22:21336586-21353321;22:21336662-21337398;22:21336662-21351637;22:21348908-21348985 CLN:1349334;dbVar:nssv17974796 22:21337344-21337343;22:21337344-21337456 22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) dbVar:nssv15161990;dbVar:nssv15139753;dbVar:nssv15150031;dbVar:nssv15150491;dbVar:nssv15146973;dbVar:nssv15135173;dbVar:nssv15137211;dbVar:nssv15129128;dbVar:nssv15161991;dbVar:nssv15161992;dbVar:nssv15164031;dbVar:nssv16254742;dbVar:nssv16297047;dbVar:nssv15151140;nssv16207460;dbVar:nssv15141953;dbVar:nssv15156366;nssv15772157;dbVar:nssv17976875;dbVar:nssv16207463;dbVar:nssv16296938;dbVar:nssv16207464;dbVar:nssv15774756;dbVar:nssv18329565;dbVar:nssv15149512;nssv15150794;dbVar:nssv15139758;dbVar:nssv15755803;dbVar:nssv15774287;dbVar:nssv15605979;dbVar:nssv15139756;dbVar:nssv15605980;dbVar:nssv15137771;dbVar:nssv15132295;dbVar:nssv15133039;dbVar:nssv15133301;dbVar:nssv15132518;dbVar:nssv15134365;dbVar:nssv15146613;dbVar:nssv15133111;dbVar:nssv15147269;dbVar:nssv15121201;dbVar:nssv15136264;dbVar:nssv15605803;dbVar:nssv15605804;dbVar:nssv16736606;dbVar:nssv15128891;dbVar:nssv15126571;dbVar:nssv15128500;dbVar:nssv16254735;dbVar:nssv15140068;dbVar:nssv15137505;dbVar:nssv15128758;dbVar:nssv15152138;dbVar:nssv15154014;dbVar:nssv15755815;dbVar:nssv15755817;dbVar:nssv16255668;dbVar:nssv18329661;dbVar:nssv18330205;dbVar:nssv15156359;dbVar:nssv15142823;dbVar:nssv15140066;dbVar:nssv15133432;dbVar:nssv15605805;dbVar:nssv15605808;dbVar:nssv15605806;dbVar:nssv15132858;dbVar:nssv15133520;dbVar:nssv15132127;dbVar:nssv15133128;dbVar:nssv15136566;dbVar:nssv15133389;dbVar:nssv15140044;dbVar:nssv15133925;dbVar:nssv15138146;dbVar:nssv15133393;nssv15139545;dbVar:nssv15135020;dbVar:nssv15132566;dbVar:nssv15164039;dbVar:nssv17955656;dbVar:nssv15132423;dbVar:nssv15132330;dbVar:nssv15126758;dbVar:nssv15127771;dbVar:nssv15126436;dbVar:nssv17649918;dbVar:nssv15162011;dbVar:nssv15125959;dbVar:nssv17955842;dbVar:nssv15139556;dbVar:nssv15122631;dbVar:nssv15123767;dbVar:nssv15162014;dbVar:nssv15143627;dbVar:nssv16865904;dbVar:nssv15123759;dbVar:nssv17650003;dbVar:nssv15755805;dbVar:nssv15132167;dbVar:nssv15133526;dbVar:nssv15162019;dbVar:nssv15145463;dbVar:nssv15145234;dbVar:nssv16207634;dbVar:nssv15605810;dbVar:nssv15605809;dbVar:nssv18842027;dbVar:nssv18842024;nssv18842046;dbVar:nssv18326316;dbVar:nssv15139749;dbVar:nssv15140369;dbVar:nssv15136643;dbVar:nssv15131931;nssv15133075;dbVar:nssv15131925;dbVar:nssv15134715;dbVar:nssv15132426;TS3:ISCA-37446;dbVar:nssv15605828;dbVar:nssv15153271;dbVar:nssv17976874;dbVar:nssv15139887;dbVar:nssv15137698;dbVar:nssv15139242;dbVar:nssv18329574;dbVar:nssv18329591;dbVar:nssv17976884;dbVar:nssv15132247;nssv15139527;dbVar:nssv15131997;nssv15139348;dbVar:nssv15137835;dbVar:nssv15132026;nssv15139977;dbVar:nssv15127741;dbVar:nssv18830785;dbVar:nssv15154013;dbVar:nssv16254573;dbVar:nssv16255670;dbVar:nssv15133914;dbVar:nssv15145464;dbVar:nssv15755306;dbVar:nssv15132169;dbVar:nssv17976883;dbVar:nssv16207466;dbVar:nssv15132044;dbVar:nssv15139694;dbVar:nssv15120579;dbVar:nssv15133646;dbVar:nssv15139596;dbVar:nssv15132083;dbVar:nssv18330192;dbVar:nssv15139716;dbVar:nssv15135998;dbVar:nssv15139748 22:16054668-51243435;22:16054692-27296513;22:16054692-51220902;22:16054692-51237463;22:16054692-51237518;22:16087695-19010508;22:16087695-20311784;22:16114245-18917748;22:16114245-20737903;22:16114245-51195728;22:16114245-51211392;22:16197006-51224252;22:16800001-21500000;22:16888900-18916828;22:16888900-20311858;22:16888900-20312661;22:16888900-21915509;22:16888900-22290476;22:16888900-26483608;22:16888900-27657507;22:16888900-51197838;22:16888901-18916828;22:16888901-51197838;22:17012936-21431054;22:17041670-20247250;22:17055734-20312661;22:17072087-20130474;22:17264512-23238029;22:17289828-20311922;22:17397499-18984519;22:17397499-20311763;22:17397499-20659606;22:17397499-20708934;22:17397499-21505417;22:17397499-24754904;22:17397499-51178264;22:17397634-19584890;22:17397634-51178213;22:18533255-18942804;22:18570313-19184416;22:18609713-21408430;22:18611224-21408430;22:18628020-20311763;22:18628133-21712996;22:18628133-21900562;22:18628133-51244566;22:18628148-21722313;22:18637140-20289862;22:18640730-21465659;22:18641480-21917191;22:18644791-21465659;22:18645354-21465659;22:18648856-21461017;22:18648856-21927646;22:18648867-21465659;22:18648868-20311858;22:18648868-21798907;22:18649190-20311858;22:18650665-21440455;22:18650665-21440514;22:18650676-21455556;22:18650746-21460220;22:18650804-21386010;22:18650804-21460220;22:18651615-21440455;22:18652638-21914178;22:18660554-21455556;22:18661700-21505445;22:18661700-22905025;22:18661725-20311763;22:18661725-21025713;22:18661725-21440514;22:18661725-21461752;22:18661725-21505417;22:18661725-21661435;22:18661725-32217179;22:18675474-21465050;22:18687211-19060954;22:18704555-21411284;22:18706002-21440514;22:18713492-20412989;22:18713492-21712996;22:18713492-21917191;22:18841375-21465101;22:18844633-21463730;22:18848021-21468378;22:18873002-21469900;22:18874966-21028946;22:18877788-20306993;22:18877788-21462353;22:18878410-21467387;22:18886916-20278471;22:18886916-21461017;22:18886916-23421058;22:18889978-21463189;22:18890265-21464056;22:18890272-21505417;22:18890272-21561514;22:18891399-21463730;22:18891967-20311852;22:18891967-21631412;22:18892576-20306993;22:18892576-20308800;22:18892576-21460220;22:18893839-20508931;22:18893839-21416074;22:18893889-21414817;22:18894340-21032422;22:18894340-21440455;22:18894821-21505445;22:18894836-21505417;22:18894836-21561514;22:18894836-21809009;22:18909039-21798755;22:18912232-21465672;22:18912515-21922035;22:18916828-21465659;22:18916828-21804886;22:18916829-21465659;22:18916829-21465662;22:18916843-21465659;22:18916844-21798907;22:18916844-21804563;22:18917048-21465659;22:18919943-21505417;22:18919943-21561514;22:18919943-21801604;22:18919943-21809009;22:18919988-21561468;22:18936190-21464809;22:18970561-21465662;22:19024657-21465662;22:19035090-22672555;22:19058830-21561514;22:19346606-21864619;22:19819478-21464764;22:20402634-21561514;22:20732809-21465659;22:20732809-25193541;22:20748977-21499971;22:20754423-21505417;22:21022841-22712836;22:21025655-21505417;22:21025655-22336268;22:21025655-22400806;22:21029657-22485776;22:21081261-21505417;22:21261515-37583387;22:21400684-23654222 7.30;22.85;7.31;7.30;7.30;3.96;33.54;0.82;39.86;7.32;7.32;7.34;54.67;1.08;41.40;41.41;51.11;47.57;26.78;23.86;7.49;1.08;7.49;57.40;42.19;43.53;40.40;43.01;46.89;5.65;48.62;54.10;54.78;62.54;34.92;7.61;31.55;7.61;11.71;47.16;89.81;89.86;84.15;83.29;78.51;7.88;83.04;84.41;90.95;78.43;91.08;91.10;91.25;78.36;91.21;85.21;81.56;85.23;91.25;91.25;91.30;91.31;91.08;91.31;91.28;78.78;91.62;90.35;60.55;85.87;90.14;91.61;91.67;90.35;85.65;18.95;92.10;44.45;92.97;93.09;89.33;85.66;80.20;97.92;98.08;98.05;98.94;99.08;98.81;99.34;99.24;99.43;99.69;56.67;99.81;99.82;98.25;96.18;99.87;99.80;93.79;99.84;99.84;99.91;99.94;99.96;99.96;99.98;99.98;98.42;98.42;96.35;88.17;88.42;99.94;84.78;99.94;88.20;99.94;99.94;99.94;88.38;88.21;99.94;98.40;96.31;88.29;88.06;96.31;99.97;99.94;99.94;66.78;96.11;84.09;99.96;91.60;99.79;16.39;95.23;94.50;26.11;91.39;33.45;31.88;29.84;90.26;1.24;2.81 22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) dbVar:nssv15134634;dbVar:nssv16208592;dbVar:nssv16208593;dbVar:nssv15141423;dbVar:nssv15132388;dbVar:nssv15128094;dbVar:nssv15132068;dbVar:nssv15133055;dbVar:nssv18787557;nssv18791888;dbVar:nssv16207650;dbVar:nssv15153272;dbVar:nssv15135754;dbVar:nssv15133431;nssv15139986;dbVar:nssv15125556;dbVar:nssv15126775;dbVar:nssv15133864;dbVar:nssv15755811;dbVar:nssv15755813;dbVar:nssv18326404;dbVar:nssv15126915;dbVar:nssv15128185;dbVar:nssv15145459;dbVar:nssv15145460;dbVar:nssv15138286;dbVar:nssv15154015;nssv18326430;dbVar:nssv18330227;dbVar:nssv17976889;dbVar:nssv17976891;dbVar:nssv15153273;dbVar:nssv18330460;dbVar:nssv17976888;dbVar:nssv15145461;dbVar:nssv15138328;dbVar:nssv17976880;dbVar:nssv15154017;dbVar:nssv18329577;dbVar:nssv15140316;dbVar:nssv15133433;dbVar:nssv18326382;dbVar:nssv17955872;dbVar:nssv15133434;dbVar:nssv16255835;dbVar:nssv15132708;dbVar:nssv15134184;dbVar:nssv15132128;nssv15139349;dbVar:nssv15134982;dbVar:nssv15135883;dbVar:nssv15133394;nssv16091745;dbVar:nssv15132006;nssv15139990;dbVar:nssv15137884;dbVar:nssv15133435;dbVar:nssv18792765;dbVar:nssv15135454;dbVar:nssv15133438;nssv15140028;dbVar:nssv15132230;nssv15139684;dbVar:nssv15132655;nssv15139976;dbVar:nssv15136079;dbVar:nssv15132507;nssv15139975;dbVar:nssv15132389;dbVar:nssv17976452;dbVar:nssv15164040;dbVar:nssv15137872;dbVar:nssv16254738;dbVar:nssv15127636;dbVar:nssv15128166;dbVar:nssv15127784;dbVar:nssv16208773;dbVar:nssv15145231;dbVar:nssv15145040;dbVar:nssv18786377;dbVar:nssv15145232;dbVar:nssv15139558;dbVar:nssv15163611;dbVar:nssv16215256;dbVar:nssv15128065;dbVar:nssv17955534;dbVar:nssv15163612;dbVar:nssv15145462;dbVar:nssv15145233;dbVar:nssv15163613;dbVar:nssv15132390;dbVar:nssv15163614;dbVar:nssv15162012;dbVar:nssv15139255;dbVar:nssv15162013;dbVar:nssv15162015;dbVar:nssv17976449;dbVar:nssv17955549;dbVar:nssv15162016;nssv16215222;nssv16215239;nssv16865884;dbVar:nssv15162017;dbVar:nssv15164042;dbVar:nssv15143222;dbVar:nssv15162018;dbVar:nssv16865881;dbVar:nssv15164043;dbVar:nssv15755824;dbVar:nssv17650004;dbVar:nssv17649858;dbVar:nssv16297048;dbVar:nssv17517456;dbVar:nssv15141730;dbVar:nssv15126093;dbVar:nssv15125439;dbVar:nssv15755804;dbVar:nssv15121171;dbVar:nssv15133439;dbVar:nssv15132392;dbVar:nssv15132132;dbVar:nssv15133440;dbVar:nssv15136213;dbVar:nssv15605874;nssv15605879;dbVar:nssv17976881;dbVar:nssv15119655;dbVar:nssv18842051;dbVar:nssv17173212;dbVar:nssv17173202;dbVar:nssv18792648;dbVar:nssv16091922;dbVar:nssv15143862;dbVar:nssv17976675;dbVar:nssv18830700;dbVar:nssv18786378;dbVar:nssv18786379;dbVar:nssv15140698;dbVar:nssv15139562;dbVar:nssv15140747;dbVar:nssv15140051;dbVar:nssv15133317;nssv15143213;dbVar:nssv15131926;dbVar:nssv15605919;dbVar:nssv15755810;HI3:ISCA-37446;dbVar:nssv15139269;dbVar:nssv15137499;dbVar:nssv15138712;dbVar:nssv18330193;dbVar:nssv15139855;nssv18326386;dbVar:nssv15139854;nssv15153270;dbVar:nssv15154016;nssv17976890;dbVar:nssv15152149;dbVar:nssv15137491;dbVar:nssv18330326;dbVar:nssv18329598;dbVar:nssv18330218;dbVar:nssv15141653;dbVar:nssv15142207;dbVar:nssv15755814;dbVar:nssv15132248;nssv15139690;dbVar:nssv15134351;dbVar:nssv15132463;nssv15139699;dbVar:nssv15132523;dbVar:nssv15155695;dbVar:nssv18831006;dbVar:nssv17976279;dbVar:nssv15139289;dbVar:nssv15139467;dbVar:nssv15142401;dbVar:nssv15134356;dbVar:nssv18330006;dbVar:nssv15137446;dbVar:nssv17976741;dbVar:nssv15153268;dbVar:nssv15156357;dbVar:nssv18842023;dbVar:nssv15132608;dbVar:nssv15145465;dbVar:nssv15145466;dbVar:nssv15145235;dbVar:nssv15772502;dbVar:nssv15154008;dbVar:nssv15156354;dbVar:nssv15755308;nssv15755309;dbVar:nssv15155696;dbVar:nssv18330327;dbVar:nssv18326378;dbVar:nssv18329593;dbVar:nssv18330275;dbVar:nssv18329587;dbVar:nssv18329620;dbVar:nssv17956682;dbVar:nssv15776637;dbVar:nssv17649919;dbVar:nssv18326434;dbVar:nssv18326440;dbVar:nssv15120712;dbVar:nssv15139564;dbVar:nssv16208598;dbVar:nssv15755307;dbVar:nssv15156347;dbVar:nssv18330257;dbVar:nssv15755311;dbVar:nssv17957425;dbVar:nssv15121593;dbVar:nssv15154007;dbVar:nssv15134856;dbVar:nssv18330729;dbVar:nssv18330196;dbVar:nssv17977102 22:16087695-19363465;22:16888900-20125005;22:16888900-20730144;22:16888901-20026751;22:17019016-20718227;22:17177912-19892632;22:17397499-20311763;22:17397499-20708934;22:17565983-20052185;22:18475386-23764120;22:18626109-21800797;22:18628020-21464119;22:18628020-21505417;22:18628133-21561468;22:18628133-21883879;22:18628148-21440515;22:18631365-21800471;22:18636750-21800471;22:18639781-21910280;22:18641480-21712996;22:18641480-21722262;22:18642647-21717111;22:18642647-21742277;22:18644242-21465662;22:18644543-21465659;22:18644544-21800797;22:18644791-21798907;22:18644791-21800471;22:18644791-21915509;22:18644792-21041014;22:18645354-21800797;22:18646694-21631412;22:18648857-21465662;22:18648867-21798907;22:18648867-21800797;22:18648868-21465659;22:18650665-21440455;22:18650676-21455556;22:18655799-21726191;22:18660136-21737597;22:18660554-21455556;22:18661700-21457610;22:18661700-21505445;22:18661725-20659606;22:18661725-21440514;22:18661725-21461811;22:18661725-21464119;22:18661725-21505417;22:18661725-21561514;22:18661725-21809009;22:18671630-21536841;22:18689517-21588615;22:18706002-20311763;22:18706002-20659606;22:18706002-21025713;22:18706002-21440514;22:18706002-21464119;22:18706002-21505417;22:18706002-21809009;22:18718029-21326012;22:18728119-21811991;22:18765086-21661435;22:18765103-21661435;22:18788000-21065894;22:18788000-21468378;22:18788000-21684798;22:18789966-21591197;22:18790223-21697998;22:18820423-21477877;22:18834446-21414817;22:18834453-21575702;22:18844633-21463730;22:18844633-21608479;22:18844633-21797812;22:18848021-21468378;22:18861210-21630630;22:18861749-21463730;22:18868433-20331055;22:18868433-21477877;22:18872509-21465050;22:18874457-20306317;22:18875870-21470273;22:18875957-21466715;22:18876631-21465659;22:18878410-21465050;22:18878410-21907671;22:18884515-21484289;22:18884715-21483289;22:18886916-21463730;22:18886916-21465050;22:18886916-21467387;22:18886916-21811991;22:18889491-20312668;22:18889491-21463730;22:18889491-21466715;22:18889491-21917190;22:18889572-21464697;22:18889694-21465485;22:18889951-21466053;22:18889970-21462658;22:18890043-21440455;22:18890163-21464056;22:18890222-21561468;22:18890265-21540347;22:18890272-18999862;22:18890272-20328113;22:18890272-20659606;22:18890272-21394730;22:18890272-21461811;22:18891527-21796215;22:18892576-21460220;22:18893345-21650280;22:18893736-18924066;22:18893839-20307561;22:18893883-21563420;22:18893883-21571027;22:18893887-21386103;22:18893888-18923800;22:18893889-18973671;22:18893889-21414817;22:18893889-21481925;22:18893889-21570386;22:18894079-21414817;22:18894340-20255110;22:18894340-20255154;22:18894340-21440455;22:18894340-21440514;22:18894836-21505417;22:18894836-21561514;22:18900756-21800277;22:18912232-21465672;22:18912232-21465672;22:18916828-21465662;22:18916829-21465659;22:18916829-21465662;22:18916829-21800797;22:18916843-21465659;22:18916843-21465662;22:18916843-21798907;22:18916843-21804716;22:18916843-21804886;22:18916844-21465659;22:18916844-21800471;22:18916844-21915509;22:18917048-21465659;22:18917048-21465662;22:18919478-21800471;22:18919943-21505417;22:18919943-21505558;22:18919943-21561514;22:18919943-21809009;22:18935464-21465659;22:18936190-21464809;22:18936191-21464809;22:18970562-21465662;22:19024657-21465659;22:19024658-21465662;22:19029603-21505417;22:19046678-21465662;22:20279767-23822986;22:20310411-21804886;22:20311904-21465659;22:20311904-21800797;22:20609933-21576553;22:20659548-21561514;22:20703817-21503296;22:20703817-21631412;22:20713276-21477877;22:20716877-21465659;22:20716877-21465662;22:20716877-21798907;22:20716877-21800471;22:20716877-23819697;22:20716878-21465659;22:20725309-21465659;22:20725310-21804563;22:20725319-21800797;22:20728958-21798907;22:20728958-21800797;22:20728958-21915096;22:20729389-21465662;22:20730997-21465342;22:20732809-21465659;22:20732809-21800471;22:20733428-21505417;22:20749626-23972878;22:21029656-22481498;22:21033587-21800471;22:21049800-21465662;22:21049801-21465662;22:21059670-21800471;22:21059670-21804716;22:21065883-21937680;22:21075676-21465662;22:21081261-24593820;22:21092649-21465662;22:21188488-21804597;22:21462567-22962196 14.31;38.01;47.78;36.07;49.29;36.76;48.62;54.78;46.55;48.58;80.93;90.59;89.29;87.59;78.92;90.52;81.07;81.21;78.56;83.65;83.40;83.57;82.89;91.06;91.07;81.40;81.46;81.42;78.55;89.57;81.42;86.08;91.21;81.56;81.51;91.21;91.25;91.30;83.68;83.49;91.62;91.66;90.35;88.33;91.61;91.67;91.68;90.35;88.60;81.63;89.67;88.62;88.24;90.33;91.86;93.09;93.15;91.78;82.80;93.22;83.31;88.71;88.71;95.31;95.86;88.69;91.72;88.36;96.68;97.66;93.73;98.08;92.96;87.00;98.05;92.77;98.73;98.19;98.46;99.10;98.58;99.03;99.17;99.24;99.33;84.82;98.83;98.87;99.69;99.66;99.57;87.84;99.62;99.79;99.69;84.86;99.77;99.75;99.74;99.81;99.81;99.82;96.18;96.95;95.84;99.68;99.74;99.82;99.82;88.45;99.91;93.19;96.37;99.93;96.24;95.97;99.96;96.83;98.81;99.96;99.28;95.99;99.97;99.96;99.96;99.98;99.98;98.42;96.35;88.41;99.94;99.94;99.94;99.94;99.94;88.33;99.94;99.94;88.38;88.21;88.20;99.94;88.34;84.95;99.94;99.94;88.33;98.40;98.40;96.31;88.06;99.94;99.97;99.97;99.94;99.94;99.94;98.33;99.94;33.43;77.20;99.87;77.39;88.37;89.20;95.10;81.96;98.20;99.79;99.79;69.06;68.96;24.08;99.79;99.79;68.46;68.70;68.71;68.59;61.98;99.79;99.83;99.79;68.50;94.65;22.17;29.92;56.14;99.63;99.63;54.60;54.29;45.68;99.60;10.90;99.59;44.74;0.10 626 2-hydroxyglutaric_aciduria;Abnormality_of_metabolism/homeostasis;Acute_rhabdomyolysis;Autism_spectrum_disorder;Bardet-Biedl_syndrome;Bernard_Soulier_syndrome;CEDNIK_syndrome;CLDN5-related_neurodevelopmental_disorder;CLDN5_deficiency;Cardiac_arrhythmia;Cardiovascular_phenotype;D,L-2-hydroxyglutaric_aciduria;DiGeorge_syndrome;Emery-Dreifuss_muscular_dystrophy;Episodic_flaccid_weakness;Hereditary_cancer-predisposing_syndrome;Hypertrophic_cardiomyopathy_1;Hypomyelinating_leukodystrophy_2;Inborn_genetic_diseases;Intellectual_disability;LZTR1-related_disorder;LZTR1-related_schwannomatosis;Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation;Meier-Gorlin_syndrome_7;Metabolic_crises_with_rhabdomyolysis,_cardiac_arrhythmias,_and_neurodegeneration;Myasthenic_syndrome,_congenital,_23,_presynaptic;Neurodevelopmental_disorder;Noonan_syndrome;Noonan_syndrome_1;Noonan_syndrome_10;Noonan_syndrome_2;Noonan_syndrome_and_Noonan-related_syndrome;PI4KA-related_disorder;Polymicrogyria,_perisylvian,_with_cerebellar_hypoplasia_and_arthrogryposis;Proline_dehydrogenase_deficiency;RASopathy;Recurrent_metabolic_encephalomyopathic_crises-rhabdomyolysis-cardiac_arrhythmia-intellectual_disability_syndrome;SLC25A1-related_disorder;Schizophrenia_4;Schwannomatosis;See_cases;Seizure;Spastic_paraplegia_84,_autosomal_recessive;TANGO2-related_disorder;TBX1-related_disorder;Thrombocytopenia;Van_den_Ende-Gupta_syndrome;Velocardiofacial_syndrome;not_specified IMH 22:17036164-22613666 0.1686 22:18667571-18994853 DDD:56146;22:18877788-19033532 dgv543n27;22:18884850-18926400 gnomAD-SV_v2.1_DUP_22_50647;22:18912158-18998999 esv3647250;22:19148049-19148136 gnomAD-SV_v2.1_DUP_22_50677;22:20062642-20063204 IMH;22:20313251-20369884 DDD:56225;22:20330330-20450295 DDD:56232;22:20659548-20717455 DDD:56255;22:21033800-21039000 gnomAD-SV_v2.1_DUP_22_50819;22:21383283-21845355 esv2760719 22:18655861-19006984 dgv99e203;22:18876429-19006125 DDD:56173;22:18882313-19012377 DDD:56174;22:18912158-18998999 1000g;22:18924000-18940000 gnomAD-SV_v2.1_DUP_22_50652;22:19702276-19702320 DDD:56203;22:20067805-20068161 DDD:56218;22:20322450-20718598 DDD:56226;22:20343574-20380608 DDD:56234;22:20705946-20718598 DDD:56260;22:21088868-21089010 DDD:56283 chr22:18884925-18927000 dbVar;chr22:18912157-18998999 dbVar;chr22:18920358-18923595 dbVar;chr22:18934402-18934486 dbVar;chr22:18938445-18969406 dbVar;chr22:18961454-18962214 dbVar;chr22:18977575-18977640 dbVar;chr22:18977576-18977640 dbVar;chr22:18979860-18979920 dbVar;chr22:18984228-18985696 dbVar;chr22:18994879-18998062 dbVar;chr22:18997267-19009786 dbVar;chr22:19008418-19009937 dbVar;chr22:19041070-19041296 dbVar;chr22:19050181-19050386 dbVar;chr22:19063483-19063613 dbVar;22:19063767-19063900 gnomAD-SV_v2.1_DEL_22_181349;chr22:19087245-19091323 dbVar;chr22:19091546-19099675 dbVar;chr22:19099906-19100607 dbVar... chr22:18884924-19013000 dbVar;chr22:18902898-18902992 dbVar;chr22:18912910-18913458 dbVar;chr22:18929400-18935100 dbVar;chr22:18934999-21466000 dbVar;chr22:18943458-18943555 dbVar;chr22:18961457-18962214 dbVar;22:18977576-18977640 1000g;22:18977576-18977640 gnomAD-SV_v2.1_DEL_22_181334;chr22:18980769-18984165 dbVar;chr22:18990004-18990064 dbVar;chr22:18997195-19009720 dbVar;chr22:19006733-19006786 dbVar;chr22:19008684-19010259 dbVar;chr22:19050028-19050086 dbVar;chr22:19054635-19055096 dbVar;chr22:19063767-19063900 dbVar;chr22:19085539-19085825 dbVar;chr22:19091504-19102801 dbVar;22:19098616-19100995 dgv1286e212... 0.445 0.320 22:18894850-18894969 L1ME2z 22:21464126-21464591 L1MA7 22:18889511-18912230 1 97.89 -0.807902299547855 -1.20830830104818 -0.791505674827999 2.94244265911253 5.29477062168781 606810;190315;603465;138720;602054;606448;116790;616830;605566;613619;600286;142360;604202;600574 yes yes 0 1.0000e+00 1.0000e+00 1.9 1A (cf Gene_count, RE_gene, +0.00);2A (cf P_loss_source, +1.00);3C (78 genes, +0.90);5F (+0.00) 5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR6 NM_005675 6 18893832 18899601 4766 392 59 yes 5 intron2-txEnd CDS-3'UTR 597 5' 18894835 18899601 DDD:56146;DDD:56173;DDD:56174;dgv543n27;dgv99e203;gnomAD-SV_v2.1_DUP_22_50647 22:18655861-19006984;22:18667571-18994853;22:18876429-19006125;22:18877788-19033532;22:18882313-19012377;22:18884850-18926400 0.0355 dbVar chr22:18884924-19013000;chr22:18884925-18927000 0.01 IMH 22:17036164-22613666;22:18655109-20719124 0.1686 61.1 -0.678746019468492 -0.22775445384527 8214 HGNC:2846 9 9.8176e-12 7.6210e-07 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 PRODH NM_016335 6 18900293 18923806 23513 1803 100 no 14 txStart-txEnd 5'UTR-3'UTR 18900293 18923806 dbVar:nssv17649973;dbVar:nssv17971399 22:18900295-18923806;22:18910311-18923800 11 Inborn_genetic_diseases;Proline_dehydrogenase_deficiency;Schizophrenia_4 DDD:56146;DDD:56173;DDD:56174;dgv543n27;dgv99e203;gnomAD-SV_v2.1_DUP_22_50647 22:18655861-19006984;22:18667571-18994853;22:18876429-19006125;22:18877788-19033532;22:18882313-19012377;22:18884850-18926400 0.0355 dbVar chr22:18884924-19013000;chr22:18884925-18927000 0.01 IMH 22:17036164-22613666;22:18655109-20719124 0.1686 30 0 45.38 0.360135634788785 0.772811927860626 hyperprolinemia type 1 AR Definitive;Strong;Supportive 10192398;12217952;12525555;15662599;19736351;20524212;20524212[PMID]_23462603[PMID];23462603;26978485;28202261;28851938;5031477 5625 HGNC:9453 606810 Hyperprolinemia, type I, 239500 (3) AR;(Schizophrenia, susceptibility to, 4), 600850 (3) AD AD;AR yes yes 6 5.3577e-12 4.7536e-06 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LOC122455341 NR_173081 1 18926981 18935206 8225 0 0 NA 2 txStart-txEnd UTR 18926981 18935206 1000g;DDD:56146;DDD:56173;DDD:56174;dgv543n27;dgv99e203;esv3647250;gnomAD-SV_v2.1_DUP_22_50652 22:18655861-19006984;22:18667571-18994853;22:18876429-19006125;22:18877788-19033532;22:18882313-19012377;22:18912158-18998999;22:18912158-18998999;22:18924000-18940000 0.0355 dbVar chr22:18884924-19013000;chr22:18912157-18998999 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851 0.1686 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR5 NR_110533 2 18957980 19018755 60775 0 0 NA 6 txStart-txEnd UTR 18957980 19018755 dgv543n27 22:18877788-19033532 0.0100 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847 0.4801 26220 HGNC:16757 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM246C NM_001396027 1 19017036 19017734 698 696 100 no 3 txStart-txEnd 5'UTR-3'UTR 19017036 19017734 dgv543n27 22:18877788-19033532 0.0100 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 117134596 HGNC:54842 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR2 NM_005137 3 19023798 19109925 86127 1653 100 no 10 txStart-txEnd 5'UTR-3'UTR 19023798 19109925 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 39.12 -0.375038933750903 0.817637812863819 schizophrenia AD Limited 9993 HGNC:2845 4 5.1573e-06 1.0959e-03 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR11 NR_024157 1 19033674 19035888 2214 0 0 NA 1 txStart-txEnd UTR 19033674 19035888 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 25786 HGNC:17226 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 ESS2 NM_022719 3 19117791 19132164 14373 1431 100 no 10 txStart-txEnd 5'UTR-3'UTR 19117791 19132164 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 8220 HGNC:16817 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TSSK2 NM_053006 5 19118820 19120135 1315 1077 88 no 1 txStart-txEnd 5'UTR-3'UTR 19118820 19120135 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 33.13 -2.62354415217069 -2.53125239294469 -2.47162789907313 -0.184731887964386 1.02819617031079 23617 HGNC:11401 6 3.8610e-03 4.1565e-03 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 GSC2 NM_005315 2 19134505 19137805 3300 618 100 no 3 txStart-txEnd 5'UTR-3'UTR 19134505 19137805 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 65.74 1.18735715980007 0.932740471460801 2928 HGNC:4613 9 4.4347e-03 3.7186e-02 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LINC01311 NR_103767 1 19159218 19160345 1127 0 0 NA 1 txStart-txEnd UTR 19159218 19160345 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 100652736 HGNC:50503 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SLC25A1 NM_001256534 2 19163093 19166018 2925 957 100 no 8 txStart-txEnd 5'UTR-3'UTR 19163093 19166018 9 2-hydroxyglutaric_aciduria;D,L-2-hydroxyglutaric_aciduria;Inborn_genetic_diseases;Myasthenic_syndrome,_congenital,_23,_presynaptic;SLC25A1-related_disorder dbVar chr22:18934999-21466000;chr22:19161075-19192940 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 30 46.07 -2.62354415217069 -2.53125239294469 -2.47162789907313 0.459211010381399 1.99698466418685 D,L-2-hydroxyglutaric aciduria;mitochondrial disease;myasthenic syndrome, congenital, 23, presynaptic;presynaptic congenital myasthenic syndrome AD;AR Definitive;Limited;Strong;Supportive 23561848;23561848[PMID]_23393310[PMID];26273529;26870663;29238895;31527857;31808147;NULL 6576 HGNC:10979 190315 Combined D-2- and L-2-hydroxyglutaric aciduria, 615182 (3) AR;Myasthenic syndrome, congenital, 23, presynaptic, 618197 (3) AR AR yes 3 5.8829e-02 6.3354e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 CLTCL1 NM_007098 4 19166985 19279242 112257 4923 100 no 33 txStart-txEnd 5'UTR-3'UTR 19166985 19279242 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 72.86 -2.62354415217069 -2.53125239294469 -2.47162789907313 -0.597972033048653 -1.19469008098196 congenital insensitivity to pain with severe intellectual disability;multiple congenital anomalies/dysmorphic syndrome AD;AR Limited;Supportive 26068709[PMID] 8218 HGNC:2093 5 2.5101e-37 1.2408e-26 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 HIRA NM_003325 4 19318220 19419256 101036 3054 100 no 25 txStart-txEnd 5'UTR-3'UTR 19318220 19419256 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 0 0 19.48 -2.51547904504873 -2.53125239294469 -2.47162789907313 -0.543665561522748 3.98018572942351 neurodevelopmental disorder AD Limited 33417013 7290 HGNC:4916 0 1.0000e+00 1.0000e+00 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MRPL40 NM_003776 4 19420067 19423598 3531 621 100 no 4 txStart-txEnd 5'UTR-3'UTR 19420067 19423598 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 54.99 -2.62354415217069 -2.53125239294469 -2.47162789907313 0.0822917398873284 -0.450618700229176 64976 HGNC:14491 4 5.2924e-02 2.0082e-02 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 C22orf39 NM_173793 5 19428408 19435234 6826 318 100 no 3 txStart-txEnd 5'UTR-3'UTR 19428408 19435234 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 70.45 -2.53806827104914 -2.53125239294469 -2.47162789907313 0.128056348383697 0.836381939603491 128977 HGNC:27012 9 1.9976e-05 3.6900e-07 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 UFD1-AS1 NR_186687 1 19434956 19439211 4255 0 0 NA 2 txStart-txEnd UTR 19434956 19439211 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 105372860 HGNC:55917 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 UFD1 NM_005659 7 19437433 19466716 29283 924 100 no 12 txStart-txEnd 5'UTR-3'UTR 19437433 19466716 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 7353 HGNC:12520 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 CDC45 NM_001178010 2 19467348 19508135 40787 1797 100 no 20 txStart-txEnd 5'UTR-3'UTR 19467348 19508135 Meier-Gorlin syndrome 7, 617063 (3) AR dbVar:nssv15124515;morbid:CDC45 22:19467443-19508131;22:19470352-19481849 10 Meier-Gorlin_syndrome_7 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 8.4 -2.57292784443109 -2.53125239294469 -2.47162789907313 0.554183575869215 1.2901097836858 Meier-Gorlin syndrome;Meier-Gorlin syndrome 7 AD;AR Definitive;Strong;Supportive 11416137;121376;149250;27374770;27374770[PMID];282832;30986546 8318 HGNC:1739 603465 Meier-Gorlin syndrome 7, 617063 (3) AR AR yes 3 4.6237e-05 6.9104e-02 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 CLDN5 NM_001130861 1 19510546 19512860 2314 912 52 no 1 txStart-txEnd 5'UTR-3'UTR 19510546 19512860 3 CLDN5-related_neurodevelopmental_disorder;CLDN5_deficiency;Neurodevelopmental_disorder dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 50.93 2.94244265911253 3.34022892264706 neurodevelopmental disorder AD Limited 35714222;36477332 7122 HGNC:2047 1 8.9512e-01 7.4052e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LINC00895 NR_024381 1 19553652 19554362 710 0 0 NA 1 txStart-txEnd UTR 19553652 19554362 dbVar chr22:18934999-21466000;chr22:19528613-19558447;chr22:19531786-19559055 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 150185 HGNC:48580 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SEPTIN5 NM_002688 6 19702025 19710842 8817 1110 100 no 12 txStart-txEnd 5'UTR-3'UTR 19702025 19710842 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 5413 HGNC:9164 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SEPT5-GP1BB NR_037611 1 19704742 19712297 7555 0 0 NA 12 txStart-txEnd UTR 19704742 19712297 Bernard-Soulier syndrome, type B, 231200 (3) AR;Giant platelet disorder, isolated, 231200 (3) AR dbVar:nssv17977042;morbid:GP1BB 22:19711062-19712294;22:19711829-19711877 8 Bernard_Soulier_syndrome;Thrombocytopenia dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 GP1BB NM_000407 5 19711061 19712294 1233 621 100 no 2 txStart-txEnd 5'UTR-3'UTR 19711061 19712294 Bernard-Soulier syndrome, type B, 231200 (3) AR;Giant platelet disorder, isolated, 231200 (3) AR dbVar:nssv17977042;morbid:GP1BB 22:19711062-19712294;22:19711829-19711877 8 Bernard_Soulier_syndrome;Thrombocytopenia dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 30 78.01 -0.00224146961144303 0.855158778511627 Bernard-Soulier syndrome;autosomal dominant macrothrombocytopenia AD;AR Definitive;Strong;Supportive 10887115;12447957;15213102;18825380;19484238;22886561[PMID];23995613;28064200[PMID] 2812 HGNC:4440 138720 Bernard-Soulier syndrome, type B, 231200 (3) AR;Giant platelet disorder, isolated, 231200 (3) AR AR yes 7 5.1249e-01 1.0112e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TBX1 NM_001379200 1 19748300 19754857 6557 1515 100 no 7 txStart-txEnd 5'UTR-3'UTR 19748300 19754857 Conotruncal anomaly face syndrome, 217095 (3);DiGeorge syndrome, 188400 (3) AD;Tetralogy of Fallot, 187500 (3) AD;Velocardiofacial syndrome, 192430 (3) AD;DiGeorge_syndrome CLN:959024;morbid:TBX1 22:19748301-19754857;22:19748451-19748647 27 DiGeorge_syndrome;Inborn_genetic_diseases;TBX1-related_disorder;Velocardiofacial_syndrome dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 1 0 4.92 -2.62354415217069 -2.53125239294469 -2.47162789907313 2.36782594176173 3.38001100960461 22q11.2 deletion syndrome;conotruncal heart malformations;velocardiofacial syndrome AD Definitive;Strong;Supportive 11239417;11242049;11242110;11748311;14585638;14585638[PMID];18636631;192430;20054531;20937753;24637876;24998776;25860641;29500247 6899 HGNC:11592 602054 Conotruncal anomaly face syndrome, 217095 (3);DiGeorge syndrome, 188400 (3) AD;Tetralogy of Fallot, 187500 (3) AD;Velocardiofacial syndrome, 192430 (3) AD AD yes 2 8.3661e-01 9.8340e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 GNB1L NM_053004 3 19770745 19842397 71652 984 100 no 8 txStart-txEnd 5'UTR-3'UTR 19770745 19842397 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 48.57 -2.62354415217069 -2.53125239294469 -2.47162789907313 -0.373621593221624 0.590344002361273 54584 HGNC:4397 5 4.7419e-05 1.2635e-03 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 RTL10 NM_024627 6 19833668 19842397 8729 1095 82 no 3 txStart-txEnd 5'UTR-3'UTR 19833668 19842397 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 79680 HGNC:26112 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TXNRD2 NM_006440 5 19863044 19929341 66297 1575 100 no 18 txStart-txEnd 5'UTR-3'UTR 19863044 19929341 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 72.21 -2.62354415217069 -2.53125239294469 -2.47162789907313 0.348188483468328 0.327140414338646 dilated cardiomyopathy;familial glucocorticoid deficiency;familial isolated dilated cardiomyopathy;glucocorticoid deficiency 5 AD;AR Limited;Supportive 21247928[PMID];24601690[PMID];30237576;32476818 10587 HGNC:18155 606448 ?Glucocorticoid deficiency 5, 617825 (3) AR AR yes 5 3.4688e-11 1.0692e-08 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 COMT NM_000754 4 19929294 19957498 28204 816 100 no 6 txStart-txEnd 5'UTR-3'UTR 19929294 19957498 1 Bardet-Biedl_syndrome dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 40.8 -2.62354415217069 -2.53125239294469 -2.47162789907313 0.465852147917107 0.557839148920189 paroxysmal dyskinesia AD Moderate 1312 HGNC:2228 116790 (Panic disorder, susceptibility to), 167870 (3) ?AD;(Schizophrenia, susceptibility to), 181500 (3) AD ?AD;AD yes 8 1.1377e-06 8.4666e-04 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR4761 NR_039918 1 19951275 19951357 82 0 0 NA 1 txStart-txEnd UTR 19951275 19951357 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 100616414 HGNC:41591 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 ARVCF NM_001670 3 19957418 20004346 46928 2889 100 no 20 txStart-txEnd 5'UTR-3'UTR 19957418 20004346 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 54.56 -2.62354415217069 -2.53125239294469 -2.47162789907313 0.425870777992255 -0.701931719398633 421 HGNC:728 4 5.0422e-11 8.2184e-07 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TANGO2 NM_001322141 2 20008632 20054687 46055 1110 100 no 9 txStart-txEnd 5'UTR-3'UTR 20008632 20054687 Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration, 616878 (3) AR;Recurrent_metabolic_encephalomyopathic_crises-rhabdomyolysis-cardiac_arrhythmia-intellectual_disability_syndrome|Intellectual_disability|Acute_rhabdomyolysis|Episodic_flaccid_weakness|Seizure|Cardiac_arrhythmia HP:0000730;HP:0001249;HP:0001250;HP:0001267;HP:0001275;HP:0001286;HP:0001303;HP:0001656;HP:0001661;HP:0001665;HP:0001666;HP:0001687;HP:0001721;HP:0002122;HP:0002125;HP:0002182;HP:0002192;HP:0002279;HP:0002306;HP:0002316;HP:0002348;HP:0002382;HP:0002386;HP:0002391;HP:0002402;HP:0002417;HP:0002430;HP:0002431;HP:0002432;HP:0002434;HP:0002437;HP:0002458;HP:0002466;HP:0002479;HP:0002482;HP:0002499;HP:0002543;HP:0002794;HP:0003752;HP:0003767;HP:0004351;HP:0005158;HP:0006833;HP:0006997;HP:0007154;HP:0007176;HP:0007180;HP:0008942;HP:0010520;HP:0011675 CLN:226591;dbVar:nssv15770877;dbVar:nssv15772938;nssv15773614;nssv15775115;nssv15775184;nssv15775592;dbVar:nssv15772982;dbVar:nssv15775129;dbVar:nssv16216543;dbVar:nssv17171772;dbVar:nssv17971094;dbVar:nssv18790095;dbVar:nssv8639589;nssv15122532;morbid:TANGO2 22:20008633-20054687;22:20028564-20053554;22:20030823-20041691;22:20030823-20053554;22:20030859-20052185;22:20030879-20049206;22:20030879-20052185;22:20036383-20045782;22:20036384-20045781;22:20036385-20045784;22:20039969-20043556 27 Abnormality_of_metabolism/homeostasis;Acute_rhabdomyolysis;Cardiac_arrhythmia;Episodic_flaccid_weakness;Inborn_genetic_diseases;Intellectual_disability;Metabolic_crises_with_rhabdomyolysis,_cardiac_arrhythmias,_and_neurodegeneration;Recurrent_metabolic_encephalomyopathic_crises-rhabdomyolysis-cardiac_arrhythmia-intellectual_disability_syndrome;Seizure;TANGO2-related_disorder dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 51.91 -2.62354415217069 -2.53125239294469 -2.47162789907313 1.46130508236304 0.279301120222081 metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration;recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome AR Moderate;Strong 26805781;26805782 128989 HGNC:25439 616830 Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration, 616878 (3) AR AR yes 4 1.4769e-04 4.2224e-06 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR185 NR_029706 1 20020661 20020743 82 0 0 NA 1 txStart-txEnd UTR 20020661 20020743 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 406961 HGNC:31556 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR8 NM_022720 7 20067763 20099395 31632 2322 100 no 14 txStart-txEnd 5'UTR-3'UTR 20067763 20099395 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 5.07 -2.46581011772843 -2.53125239294469 -2.47162789907313 0.690563071344625 4.03153091509844 54487 HGNC:2847 0 9.9973e-01 9.9990e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR3618 NR_037412 1 20073268 20073356 88 0 0 NA 1 txStart-txEnd UTR 20073268 20073356 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 100500860 HGNC:38937 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR1306 NR_031706 1 20073580 20073665 85 0 0 NA 1 txStart-txEnd UTR 20073580 20073665 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 100302197 HGNC:35371 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TRMT2A NM_001331039 2 20099397 20104749 5352 1932 100 no 12 txStart-txEnd 5'UTR-3'UTR 20099397 20104749 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 68.23 -2.62354415217069 -2.53125239294469 -2.47162789907313 -1.98609532754524 -0.363927890852326 27037 HGNC:24974 5 1.0841e-08 1.3059e-05 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR6816 NR_106874 1 20102208 20102274 66 0 0 NA 1 txStart-txEnd UTR 20102208 20102274 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 102465490 HGNC:50256 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 RANBP1 NM_001278639 2 20103626 20114878 11252 837 100 no 6 txStart-txEnd 5'UTR-3'UTR 20103626 20114878 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 8.76 -2.62354415217069 -2.53125239294469 -2.47162789907313 -1.04492215962902 2.06932219421127 5902 HGNC:9847 2 8.2235e-01 3.3622e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SNORA77B NR_145765 1 20113924 20114049 125 0 0 NA 1 txStart-txEnd UTR 20113924 20114049 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 109617010 HGNC:52221 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 ZDHHC8 NM_001185024 2 20119326 20135530 16204 2337 100 no 11 txStart-txEnd 5'UTR-3'UTR 20119326 20135530 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 37.82 -2.62354415217069 -2.53125239294469 -2.47162789907313 -0.408428770523539 2.39258092860216 29801 HGNC:18474 1 8.5288e-01 9.8899e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 CCDC188 NM_001365892 2 20135938 20138578 2640 1209 100 no 9 txStart-txEnd 5'UTR-3'UTR 20135938 20138578 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 388849 HGNC:51899 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LINC02891 NR_038460 2 20186251 20192441 6190 0 0 NA 4 txStart-txEnd UTR 20186251 20192441 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 284865 HGNC:55221 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LINC00896 NR_026919 1 20193854 20196060 2206 0 0 NA 1 txStart-txEnd UTR 20193854 20196060 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 150197 HGNC:26519 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 RTN4R NM_023004 6 20228937 20255841 26904 1422 100 no 2 txStart-txEnd 5'UTR-3'UTR 20228937 20255841 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 35.77 -0.800223805913347 1.18081437151802 65078 HGNC:18601 605566 (Schizophrenia, susceptibility to), 181500 (3) AD AD yes 1 9.5882e-01 5.2644e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR1286 NR_031618 1 20236656 20236734 78 0 0 NA 1 txStart-txEnd UTR 20236656 20236734 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:18904624-20296851;22:18939719-20275949;22:18954422-20259184;22:18957903-20255847;22:19014638-21718005 0.4801 100302118 HGNC:35279 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 DGCR6L NM_033257 4 20301760 20307583 5823 663 100 no 5 txStart-txEnd 5'UTR-3'UTR 20301760 20307583 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 79.33 0.698499439551705 0.174075190759776 85359 HGNC:18551 7 5.0636e-05 1.2857e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM230A NR_165629 1 20326419 20350461 24042 0 0 NA 12 txStart-txEnd UTR 20326419 20350461 DDD:56225;DDD:56226 22:20313251-20369884;22:20322450-20718598 0.0509 DDD:56225;DDD:56226;dbVar chr22:18934999-21466000;22:20313251-20369884;22:20322450-20718598 0.0959 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 97.89 653203 HGNC:45045 7 4.8065e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM247B NR_186690 1 20351090 20362291 11201 0 0 NA 2 txStart-txEnd UTR 20351090 20362291 DDD:56225;DDD:56226;DDD:56232;DDD:56234 22:20313251-20369884;22:20322450-20718598;22:20330330-20450295;22:20343574-20380608 0.0509 DDD:56225;DDD:56226;DDD:56232;DDD:56234;dbVar chr22:18934999-21466000;22:20313251-20369884;22:20322450-20718598;22:20330330-20450295;22:20343574-20380608 0.0959 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 GGTLC3 NM_001355479 1 20366210 20368028 1818 678 100 no 6 txStart-txEnd 5'UTR-3'UTR 20366210 20368028 DDD:56225;DDD:56226;DDD:56232;DDD:56234 22:20313251-20369884;22:20322450-20718598;22:20330330-20450295;22:20343574-20380608 0.0509 DDD:56225;DDD:56226;DDD:56232;DDD:56234;dbVar chr22:18934999-21466000;22:20313251-20369884;22:20322450-20718598;22:20330330-20450295;22:20343574-20380608 0.0959 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 94.16 728226 HGNC:33426 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TMEM191B NM_001242313 1 20377668 20380440 2772 1041 100 no 9 txStart-txEnd 5'UTR-3'UTR 20377668 20380440 DDD:56226;DDD:56232;DDD:56234 22:20322450-20718598;22:20330330-20450295;22:20343574-20380608 0.0509 DDD:56226;DDD:56232;DDD:56234;dbVar chr22:18934999-21466000;22:20322450-20718598;22:20330330-20450295;22:20343574-20380608;chr22:20366424-20403000;chr22:20374000-20389000 0.0284 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 728229 HGNC:33600 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 PI4KAP1 NR_003563 1 20383730 20398695 14965 0 0 NA 15 txStart-txEnd UTR 20383730 20398695 DDD:56226;DDD:56232 22:20322450-20718598;22:20330330-20450295 0.0509 DDD:56226;DDD:56232;dbVar chr22:18934999-21466000;22:20322450-20718598;22:20330330-20450295;chr22:20366424-20403000 0.0189 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 728233 HGNC:33576 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 RIMBP3 NM_015672 2 20455681 20461786 6105 4920 91 no 1 txStart-txEnd 5'UTR-3'UTR 20455681 20461786 DDD:56226 22:20322450-20718598 0.0509 DDD:56226;HI40:ISCA-46728;dbVar;dgv817e199 chr22:18934999-21466000;22:20322450-20718598;22:20423846-20488792;22:20428071-20499197 0.0300 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 90.21 85376 HGNC:29344 7 9.0005e-09 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM246B NM_001396026 1 20483850 20484549 699 699 100 no 1 txStart-txEnd 5'UTR-3'UTR 20483850 20484549 DDD:56226 22:20322450-20718598 0.0509 DDD:56226;HI40:ISCA-46728;dbVar;dgv817e199 chr22:18934999-21466000;22:20322450-20718598;22:20423846-20488792;22:20428071-20499197 0.0300 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 117134597 HGNC:54843 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM230J NR_136569 2 20632119 20656858 24739 0 0 NA 9 txStart-txEnd UTR 20632119 20656858 DDD:56226 22:20322450-20718598 0.0509 DDD:56226;dbVar chr22:18934999-21466000;22:20322450-20718598 0.0118 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 729461 HGNC:52448 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 FAM230G NR_165637 1 20689194 20706786 17592 0 0 NA 7 txStart-txEnd UTR 20689194 20706786 DDD:56226;DDD:56255 22:20322450-20718598;22:20659548-20717455 0.0509 DDD:56226;DDD:56255;dbVar chr22:18934999-21466000;22:20322450-20718598;22:20659548-20717455 0.0604 IMH 22:17036164-22613666;22:18655109-20719124;22:19014638-21718005 0.1686 101927859 HGNC:52423 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 ZNF74 NM_001256524 2 20748440 20762745 14305 1935 100 no 6 txStart-txEnd 5'UTR-3'UTR 20748440 20762745 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005 0.1686 86.28 -1.30437956536809 -1.89912490049618 -1.51976012533128 2.28676628831896 2.39892044394279 7625 HGNC:13144 4 1.5586e-06 3.5588e-04 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SCARF2 NM_153334 7 20778873 20792112 13239 2607 100 no 14 txStart-txEnd 5'UTR-3'UTR 20778873 20792112 Van den Ende-Gupta syndrome, 600920 (3) AR morbid:SCARF2 22:20778874-20792112 3 Van_den_Ende-Gupta_syndrome dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005 0.1686 30 0 70.17 -1.42333559636086 -1.93669033911618 -1.61173791689534 van den Ende-Gupta syndrome AR Limited;Moderate;Strong;Supportive 20887961;20887961[PMID]_22140376[PMID];22140376;23808541;24478002;3808541 91179 HGNC:19869 613619 Van den Ende-Gupta syndrome, 600920 (3) AR AR yes 0 9.9980e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 KLHL22 NM_032775 4 20795805 20850082 54277 1905 100 no 7 txStart-txEnd 5'UTR-3'UTR 20795805 20850082 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005 0.1686 41.2 -1.60479766897668 -1.94085802577819 -1.599983320827 -0.00460568166698648 2.85964800561254 84861 HGNC:25888 2 4.2419e-01 7.0261e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MED15 NM_001003891 3 20861896 20941906 80010 2367 100 no 18 txStart-txEnd 5'UTR-3'UTR 20861896 20941906 dbVar chr22:18934999-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005 0.1686 24.41 0.672972182845271 2.65389095774821 51586 HGNC:14248 0 9.9974e-01 9.6081e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 POM121L4P NR_024592 1 21043842 21046009 2167 0 0 NA 1 txStart-txEnd UTR 21043842 21046009 dbVar chr22:18934999-21466000;chr22:21027000-21048000 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TMEM191A NR_026815 1 21055401 21058891 3490 0 0 NA 8 txStart-txEnd UTR 21055401 21058891 dbVar chr22:18934999-21466000;chr22:21052000-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 84222 HGNC:25317 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 PI4KA NM_058004 4 21061978 21213099 151121 6309 100 no 55 txStart-txEnd 5'UTR-3'UTR 21061978 21213099 Gastrointestinal defects and immunodeficiency syndrome 2, 619708 (3) AR;Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, 616531 (3) AR;Spastic paraplegia 84, AR, 619621 (3) AR;Thrombophilia 10 due to heparin cofactor II deficiency, 612356 (3) AD morbid:PI4KA;morbid:SERPIND1 22:21061979-21213099;22:21128401-21142008 8 PI4KA-related_disorder;Polymicrogyria,_perisylvian,_with_cerebellar_hypoplasia_and_arthrogryposis;Spastic_paraplegia_84,_autosomal_recessive dbVar chr22:18934999-21466000;chr22:21052000-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 35.17 1.20573288011437 5.29477062168781 polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis AR Moderate;Strong 25855803;29738522;30614210;34415310;34415322 5297 HGNC:8983 600286 Gastrointestinal defects and immunodeficiency syndrome 2, 619708 (3) AR;Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, 616531 (3) AR;Spastic paraplegia 84, AR, 619621 (3) AR AR yes 2 3.1234e-12 8.0407e-04 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SERPIND1 NM_000185 4 21128400 21142008 13608 1500 100 no 5 txStart-txEnd 5'UTR-3'UTR 21128400 21142008 Thrombophilia 10 due to heparin cofactor II deficiency, 612356 (3) AD morbid:SERPIND1 22:21128401-21142008 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21078735-21159481 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 68.88 -1.06265755233802 -1.49456297636655 -1.03231231326932 -0.289055396385536 -0.349034099945665 heparin cofactor 2 deficiency AD Definitive;Limited;Strong 15337701;2647747;277130;8562924 3053 HGNC:4838 142360 Thrombophilia 10 due to heparin cofactor II deficiency, 612356 (3) AD AD yes 8 2.5137e-10 2.7955e-05 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SNAP29 NM_004782 4 21213294 21245502 32208 777 100 no 5 txStart-txEnd 5'UTR-3'UTR 21213294 21245502 Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome, 609528 (3) AR morbid:SNAP29 22:21213295-21245502 15 CEDNIK_syndrome;Hypomyelinating_leukodystrophy_2;Inborn_genetic_diseases dbVar chr22:18934999-21466000;chr22:21052000-21466000 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 30 61.36 -1.39880243235913 -1.53414994058354 -1.19910660480315 1.58078637399342 -0.841707455415557 CEDNIK syndrome AR Strong;Supportive 15968592;15968592[PMID]_21073448[PMID];21073448;23231787;25473036;26747696 9342 HGNC:11133 604202 Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome, 609528 (3) AR AR yes 4 1.3567e-02 1.5166e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 CRKL NM_005207 4 21271694 21308035 36341 912 100 no 3 txStart-txEnd 5'UTR-3'UTR 21271694 21308035 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 1 0 4.35 -0.928255048107525 -1.20830830104818 -0.791505674827999 0.477351976371369 3.00980268645085 congenital heart disease No Known Disease Relationship 1399 HGNC:2363 3 4.4604e-01 1.6345e-01 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LINC01637 NR_110537 1 21311379 21318968 7589 0 0 NA 2 txStart-txEnd UTR 21311379 21318968 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 101928891 HGNC:52424 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 AIFM3 NM_144704 3 21319459 21335647 16188 1818 100 no 21 txStart-txEnd 5'UTR-3'UTR 21319459 21335647 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 38.59 -1.14442881641699 -1.26664892202732 -0.922844550293754 0.687283106386744 1.33036583543754 150209 HGNC:26398 5 1.9474e-14 1.9583e-10 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LZTR1 NM_006767 4 21336585 21353321 16736 2523 100 no 21 txStart-txEnd 5'UTR-3'UTR 21336585 21353321 Schwannomatosis CLN:906110;CLN:906111;CLN:917324 22:21344737-21344807;22:21345949-21346047;22:21348439-21348534 Noonan syndrome 10, 616564 (3) AD;Noonan syndrome 2, 605275 (3) AR;Schwannomatosis-2, susceptibility to, 615670 (3) AD CLN:2871255;dbVar:nssv17171582;dbVar:nssv17971092;morbid:LZTR1 22:21336586-21353321;22:21336662-21337398;22:21336662-21351637;22:21348908-21348985 CLN:1349334;dbVar:nssv17974796 22:21337344-21337343;22:21337344-21337456 502 Autism_spectrum_disorder;Cardiovascular_phenotype;Emery-Dreifuss_muscular_dystrophy;Hereditary_cancer-predisposing_syndrome;Hypertrophic_cardiomyopathy_1;LZTR1-related_disorder;LZTR1-related_schwannomatosis;Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation;Noonan_syndrome;Noonan_syndrome_1;Noonan_syndrome_10;Noonan_syndrome_2;Noonan_syndrome_and_Noonan-related_syndrome;RASopathy;Schwannomatosis;See_cases;not_specified dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 32.82 -1.25119505668143 -1.28020537251329 -0.946080819110286 0.246895000414255 0.909128978651125 LZTR1-related schwannomatosis;Noonan syndrome;Noonan syndrome 10;Noonan syndrome 2;breast cancer;schwannomatosis AD;AR Definitive;Moderate;Strong;Supportive 15955931;16534111;23401320;24362817;25335493;25480913;25795793;25795793[PMID];26446362;274799;278971;287232;29469822;29959388;30368668;303983;30442762;30442766;30481304;30859559;31182298;37592023;37936555;38135892 8216 HGNC:6742 600574 Noonan syndrome 10, 616564 (3) AD;Noonan syndrome 2, 605275 (3) AR;(Schwannomatosis-2, susceptibility to), 615670 (3) AD AD;AR yes yes 9 1.0211e-92 3.3832e-52 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 THAP7 NM_030573 3 21353392 21356407 3015 930 100 no 4 txStart-txEnd 5'UTR-3'UTR 21353392 21356407 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 50.87 -1.44618961523547 -1.52989215323949 -1.19895133869269 -1.50983365445593 1.16392737773964 80764 HGNC:23190 4 1.3291e-02 2.9328e-02 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 THAP7-AS1 NR_027051 1 21356210 21364663 8453 0 0 NA 2 txStart-txEnd UTR 21356210 21364663 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 439931 HGNC:41013 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 TUBA3FP NR_003608 1 21362491 21368576 6085 0 0 NA 3 txStart-txEnd UTR 21362491 21368576 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776;chr22:21358356-21370047;chr22:21360600-21369738 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 113691 HGNC:24067 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 P2RX6 NM_001394691 1 21369453 21382297 12844 1422 100 no 12 txStart-txEnd 5'UTR-3'UTR 21369453 21382297 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 76.26 -1.8606303493434 -1.51336493990188 -1.2805127161158 -0.990180484365383 -0.63060581685217 myopathy AR Limited 9127 HGNC:8538 6 4.4680e-09 1.8785e-07 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 SLC7A4 NM_004173 3 21383006 21386850 3844 1908 100 no 5 txStart-txEnd 5'UTR-3'UTR 21383006 21386850 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 74.02 -0.807902299547855 -1.26588610868392 -1.04316708587741 -0.387275128092876 -1.12481109733158 6545 HGNC:11062 6 2.8317e-07 1.0047e-04 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 MIR649 NR_030379 1 21388464 21388561 97 0 0 NA 1 txStart-txEnd UTR 21388464 21388561 esv2760719 22:21383283-21845355 0.0100 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 693234 HGNC:32905 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 P2RX6P NR_002829 1 21396680 21398538 1858 0 0 NA 2 txStart-txEnd UTR 21396680 21398538 esv2760719 22:21383283-21845355 0.0100 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 440799 HGNC:34076 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 LRRC74B NM_001291006 2 21400234 21418457 18223 1179 100 no 10 txStart-txEnd 5'UTR-3'UTR 21400234 21418457 esv2760719 22:21383283-21845355 0.0100 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21256865-21435776 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 400891 HGNC:34301 full=5
22_18894836_21464119_DEL_1 22 18894836 21464119 -2569284 DEL Di George syndrom Pathogenic NA split q11.21 BCRP2 NR_037566 1 21457304 21476575 6815 0 0 NA 6 txStart-intron1 UTR 6098 3' 21457304 21464119 esv2760719 22:21383283-21845355 0.0100 dbVar chr22:18934999-21466000;chr22:21052000-21466000;chr22:21455959-21464881;chr22:21456000-21467000 0.01 IMH 22:17036164-22613666;22:19014638-21718005;22:21042853-21483407 0.1686 400892 HGNC:1015 full=5
4_71553_9371067_DEL_1 4 71553 9371067 -9299515 DEL 4p- syndrom Pathogenic NA full p16.3-p16.1 ZNF595;ZNF718;ZNF876P;ZNF732;ZNF141;MIR571;ABCA11P;ZNF721;PIGG;TMEM271;LOC105374338;PDE6B;PDE6B-AS1;ATP5ME;MYL5;SLC49A3;PCGF3;PCGF3-AS1;CPLX1;GAK;TMEM175;DGKQ;SLC26A1;IDUA;FGFRL1;RNF212;LOC105374344;TMED11P;SPON2;LOC100130872;CTBP1-AS;CTBP1;CTBP1-DT;MAEA;UVSSA;NKX1-1;FAM53A;SLBP;TMEM129;TACC3;FGFR3;LETM1;NSD2;SCARNA22;NELFA;MIR943;NICOL1;NAT8L;POLN;HAUS3;MXD4;MIR4800;ZFYVE28;CFAP99;RNF4;FAM193A;TNIP2;SH3BP2;ADD1;MFSD10;NOP14-AS1;NOP14;GRK4;HTT-AS;HTT;MSANTD1;RGS12;HGFAC;DOK7;LRPAP1;LINC00955;LINC02171;ADRA2C;FAM86EP;OTOP1;TMEM128;LYAR;ZBTB49;NSG1;STX18;STX18-IT1;STX18-AS1;SNORD162;LOC101928279;LINC01396;MSX1;LOC101928306;CYTL1;STK32B;LINC01587;EVC2;EVC;CRMP1;MIR378D1;C4orf50;JAKMIP1;LOC128125818;JAKMIP1-DT;WFS1;PPP2R2C;MAN2B2;MRFAP1;LINC02482;MRFAP1L2;LINC02481;S100P;MRFAP1L1;BLOC1S4;KIAA0232;TBC1D14;LOC100129931;CFAP184;TADA2B;GRPEL1;LINC02447;SORCS2;MIR4798;PSAPL1;MIR4274;AFAP1-AS1;AFAP1;LOC389199;ABLIM2;MIR95;SH3TC1;HTRA3;LINC02517;ACOX3;TRMT44;GPR78;CPZ;LOC101928532;HMX1;FAM90A26;USP17L10;USP17L11;USP17L12;USP17L13;USP17L15;USP17L17;USP17L18;USP17L19;USP17L20;USP17L21;USP17L22;USP17L24;USP17L25;USP17L26;USP17L5;USP17L27;USP17L28;USP17L29;USP17L9P;USP17L30;USP17L6P DEFB131A 155 ACACA (morbid/RE=mTL_miRNA);ACTC1 (morbid/RE=mTL_miRNA);ACVR1 (morbid/RE=mTL_miRNA);AGO2 (morbid/RE=mTL_miRNA);AKT1 (morbid/RE=mTL_miRNA);ANTXR2 (morbid/RE=mTL_miRNA);ARF1 (morbid/RE=mTL_miRNA);ARHGDIA (morbid/RE=mTL_miRNA);ARL6IP1 (morbid/RE=mTL_miRNA);ARPC1B (morbid/RE=mTL_miRNA);ATXN2 (morbid/RE=mTL_miRNA);CAD (morbid/RE=mTL_miRNA);CALM2 (morbid/RE=mTL_miRNA);CASK (morbid/RE=mTL_miRNA);CCNF (morbid/RE=mTL_miRNA);CELF2 (morbid/RE=mTL_miRNA);CEP55 (morbid/RE=mTL_miRNA);CIITA (morbid/RE=mTL_miRNA);CNTNAP2 (morbid/RE=mTL_miRNA);COL18A1 (morbid/RE=mTL_miRNA);COL1A1 (HI=3/morbid/RE=mTL_miRNA);CREBBP (HI=3/morbid/RE=mTL_miRNA);CTCF (HI=3/morbid/RE=mTL_miRNA);DAAM2 (morbid/RE=mTL_miRNA);DDR2 (morbid/RE=mTL_miRNA);DDX3X (HI=3/morbid/RE=mTL_miRNA);EDEM3 (morbid/RE=mTL_miRNA);EGLN1 (morbid/RE=mTL_miRNA);ELOVL5 (morbid/RE=mTL_miRNA);ESCO2 (morbid/RE=mTL_miRNA);FBXO22 (morbid/RE=mTL_miRNA);FICD (morbid/RE=mTL_miRNA);FLCN (HI=3/morbid/RE=mTL_miRNA);FLVCR1 (morbid/RE=mTL_miRNA);FOXC1 (HI=3/morbid/RE=mTL_miRNA);FOXP2 (HI=3/morbid/RE=mTL_miRNA);G6PD (morbid/RE=mTL_miRNA);GABRB2 (morbid/RE=mTL_miRNA);GATA6 (HI=3/morbid/RE=mTL_miRNA);GLI2 (HI=3/morbid/RE=mTL_miRNA);GLUL (morbid/RE=mTL_miRNA);GNAS (HI=3/morbid/RE=mTL_miRNA);HERC2 (morbid/RE=mTL_miRNA);HFE (morbid/RE=mTL_miRNA);IGF1R (HI=3/morbid/RE=mTL_miRNA);INF2 (morbid/RE=mTL_miRNA);ITM2B (morbid/RE=mTL_miRNA);KCNJ6 (morbid/RE=mTL_miRNA);LAMA4 (morbid/RE=mTL_miRNA);LMNB2 (morbid/RE=mTL_miRNA)... Retinitis_pigmentosa_40;Retinitis_pigmentosa|Retinitis_pigmentosa_40 HP:0000547 CLN:28147;CLN:801370;dbVar:nssv15124412;dbVar:nssv15130095;dbVar:nssv15132150;dbVar:nssv15132411;dbVar:nssv15132589;dbVar:nssv15133497;dbVar:nssv15153559;dbVar:nssv15161020;dbVar:nssv16255833;dbVar:nssv16867404;dbVar:nssv17172169;dbVar:nssv17973849;dbVar:nssv18330201 4:127234-8667610;4:1420949-1836794;4:1737489-1808653;4:1770487-2303110;4:374558-745174;4:5567009-5587839;4:5785270-5803831;4:614356-2959936;4:619584-619584;4:619584-619655;4:619590-619662;4:72448-3848881;4:72448-5608810;4:85041-4597934;4:963689-2913553 4p16.3 terminal (Wolf-Hirschhorn syndrome) region;?Cataract 41, 116400 (3) AD;Deafness, AD 6;14;38, 600965 (3) AD;Wolfram syndrome 1, 222300 (3) AR;Wolfram-like syndrome, AD, 614296 (3) AD;Diabetes mellitus, noninsulin-dependent, association with, 125853 (3) AD;?Spermatogenic failure 62, 619673 (3) AR;Recombination rate QTL 1, 612042 (3);?Weyers acrofacial dysostosis, 193530 (3) AD;Ellis-van Creveld syndrome, 225500 (3) AR;Achondroplasia, 100800 (3) AD;Bladder cancer, somatic, 109800 (3);CATSHL syndrome, 610474 (3) AD,AR;Cervical cancer, somatic, 603956 (3);Colorectal cancer, somatic, 114500 (3);Crouzon syndrome with acanthosis nigricans, 612247 (3) AD;Hypochondroplasia, 146000 (3) AD;LADD syndrome 2, 620192 (3) AD;Muenke syndrome, 602849 (3) AD;Nevus, epidermal, somatic, 162900 (3);SADDAN, 616482 (3) AD;Spermatocytic seminoma, somatic, 273300 (3);Thanatophoric dysplasia, type I, 187600 (3) AD;Thanatophoric dysplasia, type II, 187601 (3) AD;Cherubism, 118400 (3) AD;Congenital disorder of glycosylation type 1EE with or without immunodeficiency, 621140 (3) AR;Developmental and epileptic encephalopathy 63, 617976 (3) AR;Ectodermal dysplasia 3, Witkop type, 189500 (3) AD;Orofacial cleft 5, 608874 (3) AD;Tooth agenesis, selective, 1, with or
gitextract_mvkn4kk8/
├── .gitignore
├── License.txt
├── Makefile
├── README.md
├── Scoring_Criteria_AnnotSV_v3.4.xlsx
├── bin/
│ ├── AnnotSV
│ └── INSTALL_annotations.sh
├── changeLog.txt
├── commandLineOptions.txt
├── etc/
│ └── AnnotSV/
│ ├── application.properties
│ └── configfile
├── share/
│ ├── bash/
│ │ └── AnnotSV/
│ │ ├── checkPhenoGeniusCliInstall.sh
│ │ └── searchForAFreePortNumber.bash
│ ├── doc/
│ │ └── AnnotSV/
│ │ ├── Example/
│ │ │ ├── README.commands
│ │ │ ├── test1.annotated.tsv
│ │ │ ├── test1.annotated.variantconvert.log
│ │ │ ├── test1.annotated.vcf
│ │ │ ├── test1.bed
│ │ │ ├── test2.annotated.tsv
│ │ │ ├── test2.annotated.variantconvert.log
│ │ │ ├── test2.annotated.vcf
│ │ │ └── test2.vcf
│ │ ├── annotations.md
│ │ ├── quickstart.md
│ │ ├── ranking.md
│ │ └── webserver_overview.md
│ └── tcl/
│ └── AnnotSV/
│ ├── AnnotSV-benignsv.tcl
│ ├── AnnotSV-candidategenes.tcl
│ ├── AnnotSV-clingen.tcl
│ ├── AnnotSV-closestgenes.tcl
│ ├── AnnotSV-config.tcl
│ ├── AnnotSV-cosmic.tcl
│ ├── AnnotSV-cytoband.tcl
│ ├── AnnotSV-encodeblacklist.tcl
│ ├── AnnotSV-exac.tcl
│ ├── AnnotSV-exomiser.tcl
│ ├── AnnotSV-extann.tcl
│ ├── AnnotSV-filteredVCF.tcl
│ ├── AnnotSV-gap.tcl
│ ├── AnnotSV-gccontent.tcl
│ ├── AnnotSV-gencc.tcl
│ ├── AnnotSV-general.tcl
│ ├── AnnotSV-genes.tcl
│ ├── AnnotSV-haploinsufficiency.tcl
│ ├── AnnotSV-help.tcl
│ ├── AnnotSV-loeuf-pLI.tcl
│ ├── AnnotSV-ncbi.tcl
│ ├── AnnotSV-omim.tcl
│ ├── AnnotSV-pathogenicsnvindel.tcl
│ ├── AnnotSV-pathogenicsv.tcl
│ ├── AnnotSV-phenogenius.tcl
│ ├── AnnotSV-ranking.tcl
│ ├── AnnotSV-regulatoryelements.tcl
│ ├── AnnotSV-repeat.tcl
│ ├── AnnotSV-segdup.tcl
│ ├── AnnotSV-tad.tcl
│ ├── AnnotSV-userBED.tcl
│ ├── AnnotSV-variantconvert.tcl
│ ├── AnnotSV-vcf.tcl
│ ├── AnnotSV-write.tcl
│ ├── Scripts/
│ │ └── lift_Over_a_BED_file.tcl
│ └── tcllib/
│ ├── csv/
│ │ ├── csv.tcl
│ │ └── pkgIndex.tcl
│ ├── http/
│ │ ├── autoproxy.tcl
│ │ └── pkgIndex.tcl
│ ├── json/
│ │ ├── json.tcl
│ │ ├── json_tcl.tcl
│ │ ├── json_write.tcl
│ │ ├── jsonc.tcl
│ │ └── pkgIndex.tcl
│ └── tar/
│ ├── pkgIndex.tcl
│ └── tar.tcl
└── tests/
└── AnnotSV/
├── README
├── scripts/
│ ├── check_all_public_test_directory.sh
│ ├── check_end_values.tcl
│ ├── check_includeCI.tcl
│ ├── complete_KnotAnnotSV_YAML_test.tcl
│ └── cutWithColumnNames.tcl
├── test_01_configfile/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_02_HG00096/
│ ├── command_Tcl.sh
│ ├── command_python.sh
│ └── input/
│ ├── HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.bed
│ └── HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.vcf
├── test_03_CDSandTxCoverage/
│ ├── command_Tcl.sh
│ └── input/
│ ├── control_9deletions_FCGR3A_NM_000569.bed
│ └── test_tcl.annotated.tsv.truth.sauv
├── test_04_ExternalBEDannotationFiles/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ ├── user_FtIncludedInSV.bed
│ └── user_SVincludedInFt.bed
├── test_05_BEDwithoutHeader/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ └── test.withoutHeader.bed
├── test_06_VCFfromLumpy/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.DEL.DUP.vcf
│ ├── test1.csv
│ └── test1.vcf
├── test_07_RegulatoryElement/
│ ├── command_Tcl.sh
│ └── input/
│ ├── candidateGenesFile.txt
│ ├── delMEF2C.bed
│ └── delSOX9.bed
├── test_08_largeSV/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_09_InsertionInAgene/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_10_BadVCFformat/
│ ├── command_Tcl.sh
│ └── input/
│ ├── testTRA.vcf
│ └── testVCFwithoutHeader.vcf
├── test_11_RamTracking/
│ ├── README
│ ├── commandAnnotSV.sh
│ └── command_Tcl.sh
├── test_12_SpaceSeparatedBED/
│ ├── command_Tcl.sh
│ └── input/
│ ├── space-separated.NA.bed
│ ├── space-separated.bed
│ └── tab-separated.bed
├── test_13_txFile/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.check1.bed
│ ├── test.check2.vcf
│ ├── txFile.check1.txt
│ ├── txFile.check2.txt
│ └── txFile.check3.txt
├── test_14_candidateGenesFile/
│ ├── 5
│ ├── command_Tcl.sh
│ └── input/
│ ├── candidateGenesFile.txt
│ └── test.bed
├── test_15_EmptyVCF/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.vcf
├── test_16_reciprocalYes/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.bed
│ ├── test.vcf
│ └── user_SVincludedInFt.bed
├── test_17_rankFiltering/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_18_VCFwithBrackets/
│ ├── command_Tcl.sh
│ └── input/
│ ├── INPUT_gridss_germline_output.sv.vcf
│ └── triplesvmerge.vcf
├── test_19_Mouse/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test.RE.bed
│ └── test.bed
├── test_20_MitochondrialSV/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_21_ExternalGeneAnnotationFile/
│ ├── command_Tcl.sh
│ └── input/
│ ├── configfile
│ ├── input.bed
│ └── user_annotations.tsv
├── test_22_knotAnnotSV_41SV/
│ ├── command_Tcl.sh
│ └── input/
│ ├── config_AnnotSV.tmp.yaml
│ ├── test.41_SV.bed
│ └── test.7_SV.bed
├── test_23_Exomiser/
│ ├── command_Tcl.sh
│ └── input/
│ ├── GRCh37-1SV.vcf
│ ├── GRCh37-multiSV.vcf
│ ├── GRCh38-1SV.vcf
│ └── GRCh38-multiSV.vcf
├── test_24_HtzCompound/
│ ├── command_Tcl.sh
│ └── input/
│ ├── 3samples.severalSV.vcf
│ ├── 3samples.snvindel.vcf
│ ├── 3samples.theSV.vcf
│ ├── 3samples.theSnvindel.vcf
│ ├── configfile
│ ├── test1.SV.bed
│ ├── test1.SV.vcf
│ ├── test1.SV.withoutGT.vcf
│ ├── test1.snvindel.vcf
│ └── test1.snvindel.withoutGT.vcf
├── test_25_big-ref-alt/
│ ├── command_Tcl.sh
│ └── input/
│ └── input_1-big-ref.vcf
├── test_26_HtzHomCounts_deletionFiltering/
│ ├── README
│ ├── command_Tcl.sh
│ └── input/
│ ├── 3samples.SV.vcf
│ ├── 3samples.extract-HG00096.snvindel.vcf
│ ├── SV.bed
│ ├── extract-HG00096.vcf
│ └── extract-tutu.vcf
├── test_27_Samples_ID/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test-withoutHeader.bed
│ ├── test.bed
│ └── test.vcf
├── test_28_SVsharingTheSameCoordinatesButWithDifferentSVTYPE/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_29_distNearestSS/
│ ├── command_Tcl.sh
│ └── input/
│ ├── test1.vcf
│ ├── test2.bed
│ ├── test3.bed
│ ├── test4.bed
│ ├── test5.bed
│ └── test6.bed
├── test_30_Ranking/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_31_Cytoband/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_32_metrics/
│ ├── command_Tcl.sh
│ └── input/
│ └── input.bed
├── test_33_webSiteExample/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_34_bracketedToAngularNotations/
│ ├── README
│ ├── Rodrigo_tests_ignore/
│ │ ├── Difficult/
│ │ │ ├── README
│ │ │ ├── test.vcf
│ │ │ └── test_difficult.vcf
│ │ ├── Outputs/
│ │ │ ├── command_20_square-bracketed-inv2.annotated.tsv
│ │ │ ├── input_OnlyTheReciprocalBND_square-bracketed-tra1_1.annotated.tsv
│ │ │ └── input_OnlyTheReciprocalBND_square-bracketed-tra1_2.annotated.tsv
│ │ ├── README
│ │ ├── output.csv
│ │ ├── severalSVTYPE-square-bracketed.vcf
│ │ ├── test_paired.vcf
│ │ ├── tra.output.csv
│ │ └── tra.vcf
│ ├── command_Tcl.sh
│ └── input/
│ ├── input-angle-bracketed-del_1.vcf
│ ├── input-angle-bracketed-del_partial_pass.vcf
│ ├── input-angle-bracketed-dup.vcf
│ ├── input-angle-bracketed-empty_del.vcf
│ ├── input-angle-bracketed-ins_by_gridss.vcf
│ ├── input-angle-bracketed-inv1.vcf
│ ├── input-angle-bracketed-inv2.vcf
│ ├── input-angle-bracketed-tra1.vcf
│ ├── input-angle-bracketed-tra2.vcf
│ ├── input-del_1.bed
│ ├── input-del_partial_pass.bed
│ ├── input-dup.bed
│ ├── input-empty_del.bed
│ ├── input-ins_by_gridss.bed
│ ├── input-inv1.bed
│ ├── input-square-bracketed-del_1.vcf
│ ├── input-square-bracketed-del_partial_pass.vcf
│ ├── input-square-bracketed-del_unordered.vcf
│ ├── input-square-bracketed-dup.vcf
│ ├── input-square-bracketed-empty_del.vcf
│ ├── input-square-bracketed-ins_by_gridss.vcf
│ ├── input-square-bracketed-inv1.vcf
│ ├── input-square-bracketed-inv2.vcf
│ ├── input-square-bracketed-inv3.vcf
│ ├── input-square-bracketed-tra1.vcf
│ ├── input-square-bracketed-tra2.vcf
│ ├── input-tra1.bed
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_1.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_partial_pass.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-del_unordered.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-dup.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-empty_del.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-ins_by_gridss.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-inv1.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-inv2.vcf
│ ├── input_OnlyTheReciprocalBND_square-bracketed-tra1_1.vcf
│ └── input_OnlyTheReciprocalBND_square-bracketed-tra1_2.vcf
├── test_35_phenogenius/
│ ├── command_Tcl.sh
│ └── input/
│ ├── PKD1.bed
│ └── test.bed
├── test_36_chm13/
│ ├── command_Tcl.sh
│ └── input/
│ └── test.bed
├── test_37_SVLEN/
│ ├── README
│ ├── command_Tcl.sh
│ └── input/
│ ├── input-angle-bracketed-del.vcf
│ ├── input-angle-bracketed-dup.vcf
│ ├── input-angle-bracketed-inv.vcf
│ ├── input-angle-bracketed-tra.vcf
│ ├── input-del.bed
│ ├── input-dup.bed
│ ├── input-ins_by_gridss.bed
│ ├── input-inv.bed
│ ├── input-square-bracketed-del.vcf
│ ├── input-square-bracketed-dup.vcf
│ ├── input-square-bracketed-ins_by_gridss.vcf
│ ├── input-square-bracketed-inv.vcf
│ ├── input-square-bracketed-tra.vcf
│ └── input-tra.bed
├── test_38_samePosINSwithDiffInsertedSeq/
│ ├── README
│ ├── command_Tcl.sh
│ ├── input/
│ │ ├── test_INS_1.vcf
│ │ ├── test_INS_2.vcf
│ │ └── test_INS_3.vcf
│ ├── test_INS_1.annotated.tsv
│ ├── test_INS_2.annotated.tsv
│ └── test_INS_3.annotated.tsv
└── test_39_breakpointProximity/
├── command_Tcl.sh
└── input/
├── A.bed
└── B.bed
Condensed preview — 279 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (9,528K chars).
[
{
"path": ".gitignore",
"chars": 1552,
"preview": ".pdm.toml \n\n# tests\netc/AnnotSV/configfile.minAnnotation\netc/AnnotSV/application.propertie"
},
{
"path": "License.txt",
"chars": 33093,
"preview": " GNU GENERAL PUBLIC LICENSE\r\n Version 3, 29 June 2007\r\n\r\n Copyright (C) 2007 Fr"
},
{
"path": "Makefile",
"chars": 12858,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "README.md",
"chars": 1414,
"preview": "<p align=\"center\">\n <img src=\"share/doc/AnnotSV/Images/AnnotSV_logo.png\" width=\"500\">\n\n<br />\n\n<div align=\"center\">\n "
},
{
"path": "bin/AnnotSV",
"chars": 11519,
"preview": "#!/usr/bin/env tclsh\n\n##################################################################################################"
},
{
"path": "bin/INSTALL_annotations.sh",
"chars": 1322,
"preview": "#!/bin/bash\n\n############################################################\n# Installing AnnotSV human annotations in a lo"
},
{
"path": "changeLog.txt",
"chars": 28120,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "commandLineOptions.txt",
"chars": 8260,
"preview": "\nCOMMAND LINE USAGE\n\n $ANNOTSV/bin/AnnotSV -SVinputFile 'Path of your VCF or BED input file with SV coordinates' >"
},
{
"path": "etc/AnnotSV/application.properties",
"chars": 1434,
"preview": "#\n# The Exomiser - A tool to annotate and prioritize genomic variants\n#\n# Copyright (c) 2016-2018 Queen Mary University "
},
{
"path": "etc/AnnotSV/configfile",
"chars": 5981,
"preview": "# This file is used to simplify the configuration of AnnotSV.\n# Anything behind a hashtag is considered as a comment\n# P"
},
{
"path": "share/bash/AnnotSV/checkPhenoGeniusCliInstall.sh",
"chars": 1816,
"preview": "#!/bin/bash\n\n\n# Bash script: \n# A successfully executed code should exit with code 0. \n# Other values indicate an error."
},
{
"path": "share/bash/AnnotSV/searchForAFreePortNumber.bash",
"chars": 796,
"preview": "#!/bin/bash\n\n# com: Compare two sorted files line by line. Output the lines that are common, plus the lines that are uni"
},
{
"path": "share/doc/AnnotSV/Example/README.commands",
"chars": 226,
"preview": "\n$ANNOTSV/bin/AnnotSV -SVinputFile test1.bed -outputFile ./test1.annotated.tsv -svtBEDcol 4 -genomeBuild GRCh37 -vcf 1\n\n"
},
{
"path": "share/doc/AnnotSV/Example/test1.annotated.tsv",
"chars": 558518,
"preview": "AnnotSV_ID\tSV_chrom\tSV_start\tSV_end\tSV_length\tSV_type\tBiologist_annotation\tBiologist_ranking\tSamples_ID\tAnnotation_mode\t"
},
{
"path": "share/doc/AnnotSV/Example/test1.annotated.variantconvert.log",
"chars": 158667,
"preview": "python3 /PROGS/EXTERN/AnnotSV/AnnotSV_dev/share/python3/variantconvert//src/variantconvert convert -i /PROGS/EXTERN/Anno"
},
{
"path": "share/doc/AnnotSV/Example/test1.annotated.vcf",
"chars": 542414,
"preview": "##fileformat=VCFv4.2\n##fileDate=14/04/2026\n##inputFile=/PROGS/EXTERN/AnnotSV/AnnotSV_dev/share/doc/AnnotSV/Example/test1"
},
{
"path": "share/doc/AnnotSV/Example/test1.bed",
"chars": 1854,
"preview": "# chrom\tStart\tEnd\tVariant_type\tBiologist_annotation\tBiologist_ranking\r\n1\t149041933\t149209289\tDEL\t\tBenign\r\n1\t196756231\t19"
},
{
"path": "share/doc/AnnotSV/Example/test2.annotated.tsv",
"chars": 7945,
"preview": "AnnotSV_ID\tSV_chrom\tSV_start\tSV_end\tSV_length\tSV_type\tSamples_ID\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\tsample2\tAnno"
},
{
"path": "share/doc/AnnotSV/Example/test2.annotated.variantconvert.log",
"chars": 34759,
"preview": "python3 /PROGS/EXTERN/AnnotSV/AnnotSV_dev/share/python3/variantconvert//src/variantconvert convert -i /PROGS/EXTERN/Anno"
},
{
"path": "share/doc/AnnotSV/Example/test2.annotated.vcf",
"chars": 30927,
"preview": "##fileformat=VCFv4.2\n##fileDate=14/04/2026\n##inputFile=/PROGS/EXTERN/AnnotSV/AnnotSV_dev/share/doc/AnnotSV/Example/test2"
},
{
"path": "share/doc/AnnotSV/Example/test2.vcf",
"chars": 2079,
"preview": "##fileformat=VCFv4.3\r\n##fileDate=23/03/2023\r\n##source=AnnotSV\r\n##FILTER=<ID=PASS,Description=\"Passed filter\">\r\n##ALT=<ID"
},
{
"path": "share/doc/AnnotSV/annotations.md",
"chars": 608,
"preview": "# Annotations databases\n\nAnnotSV requires different data sources for the annotation and the ranking of SV. In order to p"
},
{
"path": "share/doc/AnnotSV/quickstart.md",
"chars": 882,
"preview": "\n# Quick Installation\n\nRequirements are fully explained in the [README](../../../README.AnnotSV_3.5.7.pdf) file.\n\n1. The"
},
{
"path": "share/doc/AnnotSV/ranking.md",
"chars": 1027,
"preview": "# SV ranking/classification\n\nIn order to assist the clinical interpretation of SV, AnnotSV provides on top of the annota"
},
{
"path": "share/doc/AnnotSV/webserver_overview.md",
"chars": 3535,
"preview": "# Webserver overview\nThe AnnotSV webserver is separated into the annotation part (AnnotSV engine) and the analysis and v"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-benignsv.tcl",
"chars": 92816,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-candidategenes.tcl",
"chars": 3112,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-clingen.tcl",
"chars": 6350,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-closestgenes.tcl",
"chars": 11743,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-config.tcl",
"chars": 38975,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-cosmic.tcl",
"chars": 6052,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-cytoband.tcl",
"chars": 5174,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-encodeblacklist.tcl",
"chars": 13111,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-exac.tcl",
"chars": 11476,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-exomiser.tcl",
"chars": 17539,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-extann.tcl",
"chars": 7315,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-filteredVCF.tcl",
"chars": 10128,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-gap.tcl",
"chars": 11804,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-gccontent.tcl",
"chars": 13155,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-gencc.tcl",
"chars": 10692,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-general.tcl",
"chars": 20436,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-genes.tcl",
"chars": 32671,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-haploinsufficiency.tcl",
"chars": 4857,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-help.tcl",
"chars": 2768,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-loeuf-pLI.tcl",
"chars": 6543,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-ncbi.tcl",
"chars": 6913,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-omim.tcl",
"chars": 27479,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-pathogenicsnvindel.tcl",
"chars": 12682,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-pathogenicsv.tcl",
"chars": 40517,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-phenogenius.tcl",
"chars": 8282,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-ranking.tcl",
"chars": 54416,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-regulatoryelements.tcl",
"chars": 66225,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-repeat.tcl",
"chars": 12157,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-segdup.tcl",
"chars": 12037,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-tad.tcl",
"chars": 12853,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-userBED.tcl",
"chars": 14485,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-variantconvert.tcl",
"chars": 12318,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-vcf.tcl",
"chars": 57758,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/AnnotSV-write.tcl",
"chars": 83358,
"preview": "############################################################################################################\n# AnnotSV 3"
},
{
"path": "share/tcl/AnnotSV/Scripts/lift_Over_a_BED_file.tcl",
"chars": 4292,
"preview": "#!/usr/bin/env tclsh\n\n\n#################################################################################################"
},
{
"path": "share/tcl/AnnotSV/tcllib/csv/csv.tcl",
"chars": 20172,
"preview": "# csv.tcl --\n#\n#\tTcl implementations of CSV reader and writer\n#\n# Copyright (c) 2001 by Jeffrey Hobbs\n# Copyright ("
},
{
"path": "share/tcl/AnnotSV/tcllib/csv/pkgIndex.tcl",
"chars": 128,
"preview": "if {![package vsatisfies [package provide Tcl] 8.4]} {return}\npackage ifneeded csv 0.8.1 [list source [file join $dir cs"
},
{
"path": "share/tcl/AnnotSV/tcllib/http/autoproxy.tcl",
"chars": 18264,
"preview": "# autoproxy.tcl - Copyright (C) 2002-2008 Pat Thoyts <patthoyts@users.sf.net>\n#\n# On Unix the standard for identifying t"
},
{
"path": "share/tcl/AnnotSV/tcllib/http/pkgIndex.tcl",
"chars": 140,
"preview": "if {![package vsatisfies [package provide Tcl] 8.2]} {return}\npackage ifneeded autoproxy 1.5.3 [list source [file join $"
},
{
"path": "share/tcl/AnnotSV/tcllib/json/json.tcl",
"chars": 7663,
"preview": "# json.tcl --\n#\n#\tJSON parser for Tcl. Management code, Tcl/C detection and selection.\n#\n# Copyright (c) 2013 by Andreas"
},
{
"path": "share/tcl/AnnotSV/tcllib/json/json_tcl.tcl",
"chars": 8745,
"preview": "#\n# JSON parser for Tcl.\n#\n# See http://www.json.org/ && http://www.ietf.org/rfc/rfc4627.txt\n#\n# Total rework of t"
},
{
"path": "share/tcl/AnnotSV/tcllib/json/json_write.tcl",
"chars": 5294,
"preview": "# json_write.tcl --\n#\n#\tCommands for the generation of JSON (Java Script Object Notation).\n#\n# Copyright (c) 2009-2011 A"
},
{
"path": "share/tcl/AnnotSV/tcllib/json/jsonc.tcl",
"chars": 4237,
"preview": "# jsonc.tcl --\n#\n# Implementation of a JSON parser in C.\n#\tBinding to a yacc/bison parser by Mikhail.\n#\n# Copyrigh"
},
{
"path": "share/tcl/AnnotSV/tcllib/json/pkgIndex.tcl",
"chars": 313,
"preview": "# Tcl package index file, version 1.1\n\nif {![package vsatisfies [package provide Tcl] 8.4]} {return}\npackage ifneeded js"
},
{
"path": "share/tcl/AnnotSV/tcllib/tar/pkgIndex.tcl",
"chars": 156,
"preview": "if {![package vsatisfies [package provide Tcl] 8.4]} {\n # PRAGMA: returnok\n return\n}\npackage ifneeded tar 0.10 [li"
},
{
"path": "share/tcl/AnnotSV/tcllib/tar/tar.tcl",
"chars": 16476,
"preview": "# tar.tcl --\n#\n# Creating, extracting, and listing posix tar archives\n#\n# Copyright (c) 2004 Aaron Faupell <afa"
},
{
"path": "tests/AnnotSV/README",
"chars": 724,
"preview": "# Bash environment\n##################\n\n# The \"set -e\" option instructs bash to immediately exit if any command has a non"
},
{
"path": "tests/AnnotSV/scripts/check_all_public_test_directory.sh",
"chars": 518,
"preview": "#!/bin/bash\n\n# Timing: test_01 --> test_34 \n# 13:18:21 14:30:55\n# ~1h15\n\nfor f in test_*/command_Tcl.sh\ndo\n"
},
{
"path": "tests/AnnotSV/scripts/check_end_values.tcl",
"chars": 883,
"preview": "#!/usr/bin/env tclsh\n\nproc ContentFromFile {{Fichier \"\"}} {\n if {[string equal $Fichier \"\"]} {return \"\"}\n set f "
},
{
"path": "tests/AnnotSV/scripts/check_includeCI.tcl",
"chars": 1478,
"preview": "#!/usr/bin/env tclsh\n\nproc ContentFromFile {{Fichier \"\"}} {\n if {[string equal $Fichier \"\"]} {return \"\"}\n set f "
},
{
"path": "tests/AnnotSV/scripts/complete_KnotAnnotSV_YAML_test.tcl",
"chars": 2079,
"preview": "#!/usr/bin/env tclsh\n\n##################################################################################################"
},
{
"path": "tests/AnnotSV/scripts/cutWithColumnNames.tcl",
"chars": 1562,
"preview": "#!/usr/bin/env tclsh\n\n## Command line example:\n## /maison/geoffroy/Tcl/cutWithColumnNames.tcl test.annotated.tsv \"SV typ"
},
{
"path": "tests/AnnotSV/test_01_configfile/command_Tcl.sh",
"chars": 2201,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_01_configfile/input/test.bed",
"chars": 55,
"preview": "#chrom\tstart\tend\ttutu\tSV type\n1\t2902537\t3529849\tii\tDEL\n"
},
{
"path": "tests/AnnotSV/test_02_HG00096/command_Tcl.sh",
"chars": 4073,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_02_HG00096/command_python.sh",
"chars": 3403,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/data/scripts/cutWithColumnNames.tcl\"\nSVinputBEDfile=\"./input/HG00"
},
{
"path": "tests/AnnotSV/test_02_HG00096/input/HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.bed",
"chars": 136423,
"preview": "chrom\tstart\tend\tsvtype\n1\t3995268\t3995269\tALU;TSD=null\n1\t4204667\t4204717\tDEL\n1\t6434482\t6445321\tDEL\n1\t6438160\t6445897\tDEL\n"
},
{
"path": "tests/AnnotSV/test_02_HG00096/input/HG00096.wgs.mergedSV.v8.20130502.svs.genotypes.vcf",
"chars": 1460229,
"preview": "##fileformat=VCFv4.1\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##INFO=<ID=TSD,Number=1,Type=String,Description"
},
{
"path": "tests/AnnotSV/test_03_CDSandTxCoverage/command_Tcl.sh",
"chars": 1472,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# Check of the followin"
},
{
"path": "tests/AnnotSV/test_03_CDSandTxCoverage/input/control_9deletions_FCGR3A_NM_000569.bed",
"chars": 234,
"preview": "1\t161512000\t161512500\tDEL\n1\t161511000\t161511600\tDEL\n1\t161511000\t161512900\tDEL\n1\t161511000\t161514600\tDEL\n1\t161512500\t1615"
},
{
"path": "tests/AnnotSV/test_03_CDSandTxCoverage/input/test_tcl.annotated.tsv.truth.sauv",
"chars": 28358,
"preview": "AnnotSV_ID\tSV_chrom\tSV_start\tSV_end\tSV_length\tSV_type\tSamples_ID\tAnnotation_mode\tCytoBand\tGene_name\tClosest_left\tClosest"
},
{
"path": "tests/AnnotSV/test_04_ExternalBEDannotationFiles/command_Tcl.sh",
"chars": 2462,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n# Check the use of an ex"
},
{
"path": "tests/AnnotSV/test_04_ExternalBEDannotationFiles/input/test.bed",
"chars": 55,
"preview": "#chrom\tstart\tend\ttutu\tSV type\n1\t2902537\t3529849\tii\tDEL\n"
},
{
"path": "tests/AnnotSV/test_04_ExternalBEDannotationFiles/input/user_FtIncludedInSV.bed",
"chars": 71,
"preview": "#chrom\tstart\tend\tAAAAAAAAAAAAAAAAAAAA\n1\t3002537\t3429849\tFtIncludedInSV\n"
},
{
"path": "tests/AnnotSV/test_04_ExternalBEDannotationFiles/input/user_SVincludedInFt.bed",
"chars": 71,
"preview": "#chrom\tstart\tend\tBBBBBBBBBBBBBBBBBBBB\n1\t1902537\t4529849\tSVincludedInFt\n"
},
{
"path": "tests/AnnotSV/test_05_BEDwithoutHeader/command_Tcl.sh",
"chars": 2363,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\n# Check input BED file with header\n##################################\n# more input/te"
},
{
"path": "tests/AnnotSV/test_05_BEDwithoutHeader/input/test.bed",
"chars": 55,
"preview": "#chrom\tstart\tend\ttutu\tSV type\n1\t2902537\t3529849\tii\tDEL\n"
},
{
"path": "tests/AnnotSV/test_05_BEDwithoutHeader/input/test.withoutHeader.bed",
"chars": 25,
"preview": "1\t2902537\t3529849\tii\tDEL\n"
},
{
"path": "tests/AnnotSV/test_06_VCFfromLumpy/command_Tcl.sh",
"chars": 3005,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_06_VCFfromLumpy/input/test.DEL.DUP.vcf",
"chars": 7290,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_06_VCFfromLumpy/input/test1.csv",
"chars": 782,
"preview": "id,start_chrom,start,end_chrom,end,ref,alt,length,brackets,type_inferred\n166_1,1,67452229,1,67452635,N,[1:67452635[N,406"
},
{
"path": "tests/AnnotSV/test_06_VCFfromLumpy/input/test1.vcf",
"chars": 8375,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_07_RegulatoryElement/command_Tcl.sh",
"chars": 2820,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n# Case study 1:\n#########"
},
{
"path": "tests/AnnotSV/test_07_RegulatoryElement/input/candidateGenesFile.txt",
"chars": 12,
"preview": "CETN3 MEF2C\n"
},
{
"path": "tests/AnnotSV/test_07_RegulatoryElement/input/delMEF2C.bed",
"chars": 24,
"preview": "5\t88914328\t91802402\tDEL\n"
},
{
"path": "tests/AnnotSV/test_07_RegulatoryElement/input/delSOX9.bed",
"chars": 28,
"preview": "chr17\t68912390\t69629770\tDEL\n"
},
{
"path": "tests/AnnotSV/test_08_largeSV/command_Tcl.sh",
"chars": 997,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_08_largeSV/input/test.bed",
"chars": 52,
"preview": "1\t2806107\t107058351\t104252245\tM\tDEL\t238169240\t57\t25\n"
},
{
"path": "tests/AnnotSV/test_09_InsertionInAgene/command_Tcl.sh",
"chars": 706,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n# Check the annotation o"
},
{
"path": "tests/AnnotSV/test_09_InsertionInAgene/input/test.bed",
"chars": 46,
"preview": "11\t66278204\t66278205\t104252245\tM\t <INS>\tM\tM\tM\n"
},
{
"path": "tests/AnnotSV/test_10_BadVCFformat/command_Tcl.sh",
"chars": 2847,
"preview": "#!/bin/bash -x\n\n# The return status of the following AnnotSV command is 2 (failed).\n# It's normal and we want to continu"
},
{
"path": "tests/AnnotSV/test_10_BadVCFformat/input/testTRA.vcf",
"chars": 6486,
"preview": "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ts1\ts2\ts3\ts4\ts5\ts6\ts7\ts8\ts9\ts10\ts11\ts12\ts13\ts14\ts15\ts16\ts17\ts18\ts19\ts20\ts21"
},
{
"path": "tests/AnnotSV/test_10_BadVCFformat/input/testVCFwithoutHeader.vcf",
"chars": 293,
"preview": "1\t797179\tMantaBND:16:0:1:0:0:0:0\tT\t[8:245697[T\t231\tNoPairSupport\tSVTYPE=BND;MATEID=MantaBND:16:0:1:0:0:0:1;CIPOS=0,40;HO"
},
{
"path": "tests/AnnotSV/test_11_RamTracking/README",
"chars": 1098,
"preview": "#####################################\n## RAM tracking while running AnnotSV\n#####################################\n\n# Inp"
},
{
"path": "tests/AnnotSV/test_11_RamTracking/commandAnnotSV.sh",
"chars": 518,
"preview": "#!/bin/bash \n\nset -eo pipefail\n\ntouch \"running.flag\"\n\nSVinputFile=\"../test_02_HG00096/input/HG00096.wgs.mergedSV.v8.2013"
},
{
"path": "tests/AnnotSV/test_11_RamTracking/command_Tcl.sh",
"chars": 673,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\n# Run in background AnnotSV + creation of a flag (\"running.flag\") during the process\n"
},
{
"path": "tests/AnnotSV/test_12_SpaceSeparatedBED/command_Tcl.sh",
"chars": 2719,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_12_SpaceSeparatedBED/input/space-separated.NA.bed",
"chars": 2415,
"preview": "3 595259 660365 DEL 46.6272\tNA\n3 21802965 21809296 DEL 69.597\tNA\n4 69375345 69436236 DEL 273.905\tNA\n5 172662014 17266416"
},
{
"path": "tests/AnnotSV/test_12_SpaceSeparatedBED/input/space-separated.bed",
"chars": 2309,
"preview": "#Chrom\tStart\tEnd\tSV type\tScore\r\n3 595259 660365 DEL 46.6272\r\n3 21802965 21809296 DEL 69.597\r\n4 69375345 69436236 DEL 273"
},
{
"path": "tests/AnnotSV/test_12_SpaceSeparatedBED/input/tab-separated.bed",
"chars": 326,
"preview": "# chrom\tStart\tEnd\tVariant_type\tBiologist_annotation\tBiologist_ranking\n4\t71552\t9371067\tDEL\t4p- syndrom\tPathogenic\n5\t72319"
},
{
"path": "tests/AnnotSV/test_13_txFile/command_Tcl.sh",
"chars": 13037,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n########################"
},
{
"path": "tests/AnnotSV/test_13_txFile/input/test.check1.bed",
"chars": 110,
"preview": "#chrom\tstart\tend\tscore\tSV type\n1\t1490001\t1530001\t0222\tDUP\n1\t1570602\t1585465\tDEL\n1\t94190001\t95198431\t0.001\tDUP\n"
},
{
"path": "tests/AnnotSV/test_13_txFile/input/test.check2.vcf",
"chars": 784914,
"preview": "##fileformat=VCFv4.2\n##ALT=<ID=INV,Description=\"Inversion\">\n##FILTER=<ID=ASSEMBLY_ONLY,Description=\"Variant is supported"
},
{
"path": "tests/AnnotSV/test_13_txFile/input/txFile.check1.txt",
"chars": 37,
"preview": "dddd NM_033486.2 lll\nENST00000341832\n"
},
{
"path": "tests/AnnotSV/test_13_txFile/input/txFile.check2.txt",
"chars": 24,
"preview": "tutu\tNM_001167738\ttata\r\n"
},
{
"path": "tests/AnnotSV/test_13_txFile/input/txFile.check3.txt",
"chars": 37,
"preview": "dddd NM_033486.2 lll\nENST00000341832\n"
},
{
"path": "tests/AnnotSV/test_14_candidateGenesFile/5",
"chars": 0,
"preview": ""
},
{
"path": "tests/AnnotSV/test_14_candidateGenesFile/command_Tcl.sh",
"chars": 1964,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# -candidateGenesFile: "
},
{
"path": "tests/AnnotSV/test_14_candidateGenesFile/input/candidateGenesFile.txt",
"chars": 19,
"preview": "BBS5 CDK11A \nSSU72\n"
},
{
"path": "tests/AnnotSV/test_14_candidateGenesFile/input/test.bed",
"chars": 115,
"preview": "#chrom\tstart\tend\tscore\tSV type\n1\t1490001\t1530001\t0222\tDUP\n1\t1613810\t1687739\t0.25\tDEL\n1\t94190001\t95198431\t0.001\tDUP\n"
},
{
"path": "tests/AnnotSV/test_15_EmptyVCF/command_Tcl.sh",
"chars": 927,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\n# VCF input: \n# => contains header lines\n# => do not contain variant\n\n# => Error mess"
},
{
"path": "tests/AnnotSV/test_15_EmptyVCF/input/test.vcf",
"chars": 12743,
"preview": "##fileformat=VCFv4.2\n##ALT=<ID=INV,Description=\"Inversion\">\n##FILTER=<ID=ASSEMBLY_ONLY,Description=\"Variant is supported"
},
{
"path": "tests/AnnotSV/test_16_reciprocalYes/command_Tcl.sh",
"chars": 4472,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# -reciprocal: Use of "
},
{
"path": "tests/AnnotSV/test_16_reciprocalYes/input/test.bed",
"chars": 55,
"preview": "#chrom\tstart\tend\ttutu\tSV type\n1\t2902537\t3529849\tii\tDEL\n"
},
{
"path": "tests/AnnotSV/test_16_reciprocalYes/input/test.vcf",
"chars": 132,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n1\t2902537\t.\tN\t<DEL>\t72\tPASS\tEND=3529849;SVTYPE"
},
{
"path": "tests/AnnotSV/test_16_reciprocalYes/input/user_SVincludedInFt.bed",
"chars": 71,
"preview": "#chrom\tstart\tend\tBBBBBBBBBBBBBBBBBBBB\n1\t1902537\t4529849\tSVincludedInFt\n"
},
{
"path": "tests/AnnotSV/test_17_rankFiltering/command_Tcl.sh",
"chars": 2941,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_17_rankFiltering/input/test.bed",
"chars": 215,
"preview": "chrom\tstart\tend\tsvtype\n1\t3995268\t3995269\tALU;TSD=null\n1\t6438160\t6445897\tDEL\n1\t8200707\t8211256\tDUP\n1\t17263114\t17273513\tCN"
},
{
"path": "tests/AnnotSV/test_18_VCFwithBrackets/command_Tcl.sh",
"chars": 3337,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# The square-bracketed n"
},
{
"path": "tests/AnnotSV/test_18_VCFwithBrackets/input/INPUT_gridss_germline_output.sv.vcf",
"chars": 352622,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsampleTest\n1\t11734839\tgridss1_4o\tC\tC[1:11734958[\t53.4"
},
{
"path": "tests/AnnotSV/test_18_VCFwithBrackets/input/triplesvmerge.vcf",
"chars": 251900,
"preview": "##fileformat=VCFv4.2\r\n##FILTER=<ID=gridss_ASSEMBLY_ONLY,Description=\"Variant is supported only by assembly evidence.\">\r\n"
},
{
"path": "tests/AnnotSV/test_19_Mouse/command_Tcl.sh",
"chars": 7307,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list()"
},
{
"path": "tests/AnnotSV/test_19_Mouse/input/test.RE.bed",
"chars": 24,
"preview": "1\t20679054\t20689076\tDEL\n"
},
{
"path": "tests/AnnotSV/test_19_Mouse/input/test.bed",
"chars": 89,
"preview": "#chrom\tstart\tend\tSV type\tscore\n1\t3038297\t3156351\tDEL\t0.025\n1\t94190001\t95198035\tDUP\t0.001\n"
},
{
"path": "tests/AnnotSV/test_20_MitochondrialSV/command_Tcl.sh",
"chars": 668,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# Check with a bed cont"
},
{
"path": "tests/AnnotSV/test_20_MitochondrialSV/input/test.bed",
"chars": 24,
"preview": "M\t649\t1603\t\nM\t987\t1611\t\n"
},
{
"path": "tests/AnnotSV/test_21_ExternalGeneAnnotationFile/command_Tcl.sh",
"chars": 2183,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n#######################"
},
{
"path": "tests/AnnotSV/test_21_ExternalGeneAnnotationFile/input/configfile",
"chars": 884,
"preview": "# This file is used to simplify the configuration of AnnotSV.\n# Anything behind a hashtag is considered as a comment\n# P"
},
{
"path": "tests/AnnotSV/test_21_ExternalGeneAnnotationFile/input/input.bed",
"chars": 25,
"preview": "10\t98247690\t99268250\tDEL\n"
},
{
"path": "tests/AnnotSV/test_21_ExternalGeneAnnotationFile/input/user_annotations.tsv",
"chars": 215,
"preview": "genes\tdel.score\tdup.score\tcnv.score\nARHGAP19\t0.163145773187885\t0.339478078191488\t0.339117350686952\nPYROXD2\t0.42249188037"
},
{
"path": "tests/AnnotSV/test_22_knotAnnotSV_41SV/command_Tcl.sh",
"chars": 3891,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_22_knotAnnotSV_41SV/input/config_AnnotSV.tmp.yaml",
"chars": 7619,
"preview": "##############################################################################################\n# knotAnnotSV 1.1 "
},
{
"path": "tests/AnnotSV/test_22_knotAnnotSV_41SV/input/test.41_SV.bed",
"chars": 1854,
"preview": "# chrom\tStart\tEnd\tVariant_type\tBiologist_annotation\tBiologist_ranking\r\n1\t149041933\t149209289\tDEL\t\tBenign\r\n1\t196756231\t19"
},
{
"path": "tests/AnnotSV/test_22_knotAnnotSV_41SV/input/test.7_SV.bed",
"chars": 379,
"preview": "# chrom\tStart\tEnd\tVariant_type\tBiologist_annotation\tBiologist_ranking\r\n1\t149041933\t149209289\tDEL\t\tBenign\r\n4\t71552\t937106"
},
{
"path": "tests/AnnotSV/test_23_Exomiser/command_Tcl.sh",
"chars": 3680,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n\n######################"
},
{
"path": "tests/AnnotSV/test_23_Exomiser/input/GRCh37-1SV.vcf",
"chars": 373,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\n10\t123237900\t569156:2\tA\t]10:122457304]C\t72\tPA"
},
{
"path": "tests/AnnotSV/test_23_Exomiser/input/GRCh37-multiSV.vcf",
"chars": 1652405,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\n1\t1477855\t389:1\tG\t]1:1477984]G\t37\tPASS\tEVDNC="
},
{
"path": "tests/AnnotSV/test_23_Exomiser/input/GRCh38-1SV.vcf",
"chars": 372,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n10\t121496612\t569156:2\tA\t]10:122457304]C\t72\tPAS"
},
{
"path": "tests/AnnotSV/test_23_Exomiser/input/GRCh38-multiSV.vcf",
"chars": 1652405,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\n1\t1477855\t389:1\tG\t]1:1477984]G\t37\tPASS\tEVDNC="
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/command_Tcl.sh",
"chars": 13938,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n\n######################"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/3samples.severalSV.vcf",
"chars": 71997,
"preview": "##fileformat=VCFv4.2\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##ALT=<ID=DEL,Description=\"Deletion\">\n##ALT=<ID"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/3samples.snvindel.vcf",
"chars": 39447,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tprob\tfather\tmother\nchr1\t927744\t.\tG\tT\t3950.90\tPASS\tAC="
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/3samples.theSV.vcf",
"chars": 430,
"preview": "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tprob\nchr1\t934051\tDEL00000005\tG\t<DEL>\t.\tPASS\tIMPRECISE;SVTYPE"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/3samples.theSnvindel.vcf",
"chars": 13685,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tprob\tfather\tmother\nchr1\t925036\t.\tG\tA\t509.17\tPASS\tAC=2"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/configfile",
"chars": 3415,
"preview": "# This file is used to simplify the configuration of AnnotSV.\n# Anything behind a hashtag is considered as a comment\n# P"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/test1.SV.bed",
"chars": 24,
"preview": "2\t27313898\t27314025\tDEL\n"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/test1.SV.vcf",
"chars": 3198,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/test1.SV.withoutGT.vcf",
"chars": 3198,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/test1.snvindel.vcf",
"chars": 3126,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_24_HtzCompound/input/test1.snvindel.withoutGT.vcf",
"chars": 3126,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_25_big-ref-alt/command_Tcl.sh",
"chars": 1018,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n#######################"
},
{
"path": "tests/AnnotSV/test_25_big-ref-alt/input/input_1-big-ref.vcf",
"chars": 43531,
"preview": "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tUnnamedSample\n3\t129763380\tpbsv.DEL.7916\tCACAAAAACACGTGCACACATGCACACACAGATG"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/README",
"chars": 1179,
"preview": "# extract-HG00096.vcf extract-tutu.vcf sont quasiment les mêmes fichiers :\n# => nom de la colonne \"sample\" qui est diffé"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/command_Tcl.sh",
"chars": 8967,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n#######################"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/input/3samples.SV.vcf",
"chars": 172,
"preview": "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tprob\nchr1\t3777548\t.\tC\t<DEL>\t.\tPASS\tSVTY"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/input/3samples.extract-HG00096.snvindel.vcf",
"chars": 3192,
"preview": "##fileformat=VCFv4.1\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tprob\n1\t3809347\trs192032080\tT\tC\t100.0\tPA"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/input/SV.bed",
"chars": 44,
"preview": "1\t3777548\t4234731\tDEL\n1\t3777558\t4234720\tDUP\n"
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/input/extract-HG00096.vcf",
"chars": 4276,
"preview": "##fileformat=VCFv4.1\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00096\n1\t3777548\trs61768955\tG\tA\t100.0\tPASS\tAC=15;AF="
},
{
"path": "tests/AnnotSV/test_26_HtzHomCounts_deletionFiltering/input/extract-tutu.vcf",
"chars": 4273,
"preview": "##fileformat=VCFv4.1\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttutu\n1\t3777548\trs61768955\tG\tA\t100.0\tPASS\tAC=15;AF=0.0"
},
{
"path": "tests/AnnotSV/test_27_Samples_ID/command_Tcl.sh",
"chars": 16284,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_27_Samples_ID/input/test-withoutHeader.bed",
"chars": 70,
"preview": "13\t19341426\t19360783\tDUP\tsample1\n1\t4204667\t4204717\tDEL\tsample1,sampl2\n"
},
{
"path": "tests/AnnotSV/test_27_Samples_ID/input/test.bed",
"chars": 107,
"preview": "#Chrom\tstart\tend\tsvtype\tsamplesNames\n13\t19341426\t19360783\tDUP\tsample1\n1\t4204667\t4204717\tDEL\tsample1,sampl2\n"
},
{
"path": "tests/AnnotSV/test_27_Samples_ID/input/test.vcf",
"chars": 5656,
"preview": "##fileformat=VCFv4.2\r\n##source=LUMPY\r\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\r\n"
},
{
"path": "tests/AnnotSV/test_28_SVsharingTheSameCoordinatesButWithDifferentSVTYPE/command_Tcl.sh",
"chars": 2473,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n\n# Special case\n#######"
},
{
"path": "tests/AnnotSV/test_28_SVsharingTheSameCoordinatesButWithDifferentSVTYPE/input/test.bed",
"chars": 50,
"preview": "1\t3777548\t4234731\ttt\tDEL\n1\t3777548\t4234731\ttt\tDUP\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/command_Tcl.sh",
"chars": 10058,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n# GRCh37, NM_001037668:\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test1.vcf",
"chars": 146,
"preview": "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tALBS\nchr8\t7669129\t.\tN\t<DEL>\t12\tcnvLength\tSVTYPE=CNV;END=7669261\tGT:SM:CN:B"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test2.bed",
"chars": 25,
"preview": "12\t76738000\t76742200\tDEL\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test3.bed",
"chars": 25,
"preview": "12\t76738280\t76741600\tDEL\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test4.bed",
"chars": 26,
"preview": "2\t170343580\t170349500\tDEL\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test5.bed",
"chars": 26,
"preview": "2\t170343650\t170344315\tDEL\n"
},
{
"path": "tests/AnnotSV/test_29_distNearestSS/input/test6.bed",
"chars": 23,
"preview": "11\t7716419\t7716800\tDEL\n"
},
{
"path": "tests/AnnotSV/test_30_Ranking/command_Tcl.sh",
"chars": 1964,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n\n######################"
},
{
"path": "tests/AnnotSV/test_30_Ranking/input/test.bed",
"chars": 26,
"preview": "1\t108190708\t108194629\tDEL\n"
},
{
"path": "tests/AnnotSV/test_31_Cytoband/command_Tcl.sh",
"chars": 2040,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\n\n# Integration of cytoba"
},
{
"path": "tests/AnnotSV/test_31_Cytoband/input/test.bed",
"chars": 21,
"preview": "chr17\t1\t18960000\tDEL\n"
},
{
"path": "tests/AnnotSV/test_32_metrics/command_Tcl.sh",
"chars": 4807,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_32_metrics/input/input.bed",
"chars": 48,
"preview": "X\t96619122\t96623156\tDEL\nX\t32430304\t32431577\tDEL\n"
},
{
"path": "tests/AnnotSV/test_33_webSiteExample/command_Tcl.sh",
"chars": 1153,
"preview": "#!/bin/bash -x\n\nset -eo pipefail\n\n\ncut=\"$ANNOTSV/tests/AnnotSV/scripts/cutWithColumnNames.tcl\"\n\nfunction exists_in_list("
},
{
"path": "tests/AnnotSV/test_33_webSiteExample/input/test.bed",
"chars": 383,
"preview": "# chrom\tStart\tEnd\tVariant_type\tSamples_ID\tBiologist_annotation\tBiologist_ranking\n4\t71552\t9371067\tDEL\tsample1\t4p-syndrom\t"
},
{
"path": "tests/AnnotSV/test_34_bracketedToAngularNotations/README",
"chars": 2601,
"preview": "cd $ANNOTSV/tests/data/test_37_bracketedToAngularNotations/input/\n\n\nA same SV is described with different notations:\n- s"
},
{
"path": "tests/AnnotSV/test_34_bracketedToAngularNotations/Rodrigo_tests_ignore/Difficult/README",
"chars": 584,
"preview": "Rodrigo:\nI have attached two VCF files named \"test\" and \"test_difficult\". \nBoth are valid VCF files and contain the same"
},
{
"path": "tests/AnnotSV/test_34_bracketedToAngularNotations/Rodrigo_tests_ignore/Difficult/test.vcf",
"chars": 4008,
"preview": "##fileformat=VCFv4.1\n##contig=<ID=1,length=249250621>\n##contig=<ID=2,length=243199373>\n##contig=<ID=3,length=198022430>\n"
},
{
"path": "tests/AnnotSV/test_34_bracketedToAngularNotations/Rodrigo_tests_ignore/Difficult/test_difficult.vcf",
"chars": 2998,
"preview": "##fileformat=VCFv4.1\n##contig=<ID=1,length=249250621>\n##contig=<ID=2,length=243199373>\n##contig=<ID=3,length=198022430>\n"
},
{
"path": "tests/AnnotSV/test_34_bracketedToAngularNotations/Rodrigo_tests_ignore/Outputs/command_20_square-bracketed-inv2.annotated.tsv",
"chars": 1974,
"preview": "AnnotSV_ID\tSV_chrom\tSV_start\tSV_end\tSV_length\tSV_type\tSamples_ID\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\tAnnotat"
}
]
// ... and 79 more files (download for full content)
About this extraction
This page contains the full source code of the lgmgeo/AnnotSV GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 279 files (8.7 MB), approximately 2.3M tokens. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.