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Annotation and Ranking of Structural Variation

License: GNU General Public License v3.0

Makefile 1.23% Tcl 70.86% Shell 15.91% Dockerfile 0.19% Python 11.82%

genetics sv cnv annotation ranking priorization ngs

annotsv's Introduction

An integrated tool for Structural Variations annotation and ranking

AnnotSV Annotations Engine
AnnotSV Webserver
- Overview

Collaborative work

Anyone interested in implementing new annotations/features in AnnotSV?

Thanks to the AnnotSV user community:

- 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 :-)

annotsv's People

Contributors

Stargazers

Watchers

annotsv's Issues

Missing promotor annotations when running with "-tx ENSEMBL"

Hi,

We have AnnotSV version 2.5 running and I'm trying to run the following command:
/bin/AnnotSV -SVinputFile './input.vcf' -outputFile './output/annotSV.tsv' -tx ENSEMBL -typeOfAnnotation split -overwrite yes -hpo HP:0001234 > ./output/AnnotSV.log

couldn't open "/share/AnnotSV/Annotations_Human/FtIncludedInSV/Promoter/GRCh37/promoter.500bp.ENSEMBL.sorted.bed.tmp": read-only file system
    while executing
"open $fichier a"
    (procedure "WriteTextInFile" line 2)
    invoked from within
"WriteTextInFile [join $L_allProm "\n"] $promoterFormatted.tmp"
    (procedure "checkPromoterFile" line 49)
    invoked from within
"checkPromoterFile"
    (file "/bin/AnnotSV" line 216)

The message seems to indicate a problem with the file system, however I assume the tool won't be writing in the annotation resources, and more important; it works fine if "-tx" is set to "RefSeq"

I noticed this file in the resources:
/share/AnnotSV/Annotations_Human/FtIncludedInSV/Promoter/GRCh37/promoter.500bp.ENST.sorted.bed
Where the filename contains "ENST" instead of "ENSEMBL" (I assume the ".tmp" file is derived from this one?).
I tried running with "ENST" as value for "-tx" but it is not an allowed value.

Is this a bug, or a problem at our end?

truncated gzip input

Hello,

I'm trying to install AnnotSV 2.3 but had problems with the installation of human annotation:

tar -xf Annotations_Human_2.3.2.tar.gz -C /usr/local/usr/local/share/AnnotSV/
Annotations_Human/BreakpointsAnnotations/GCcontent/GRCh38/GRCh38_chromFa.fasta: truncated gzip input
tar: Error exit delayed from previous errors.
make: *** [install-human-annotation] Error 1

Can you please advise on how to resolve this error.

Frequency columns in annotation

Hello, thanks for tool update.
We are using filtration of AnnotSV output in our pipelines (based on annotsv_filter.cwl) and now we cannot use it's full functionality due to loss of various frequency columns.
What do you think - we should ask analysis-workflows team about new filtration, or you should reintroduce some of these columns or any other ideas?

"Known pathogenic genes or genomic regions annotation" specific to the "INV" type are missing

Hi Veronique,
I am running AnnotSV v3.0.7 but I do not see all the 16 columns concerning the "Known pathogenic genes or genomic regions annotation";
The output I've obtained only reports the first 12 columns; (the 4 columns specific to the "inv" type seem to be missed).
The documentation (page 18) mentions 12 annotation columns (cf. "Add 12 annotation columns" but actually details a list of 16 columns (4 groups of 4 columns about the "gain", "loss", "ins" and "inv" types).

print screen from the latest documentation:

I would like to double check with you if the code or the documentation needs to be updated from this observation (or perhaps did I miss a parameter in the command line).

note: all is correct about the 8 annotation columns for the "Known benign genes or genomic regions annotation"; (the 4 groups of 2 columns for the "gain", "loss", "ins" and "inv" type are all reported in the AnnotSV output.

Thank you very much,
Kind regards,

Rank 2 always missing in `ACMG_class` column

I tried out AnnotSV v3.0.4 for about 20 samples, and none of their SVs are scored rank-2 in ACMG_class column. Here is an ranks for one of the WGS samples:

$cat out.tsv | awk 'BEGIN{FS="\t"} {if ($16=="full") {print $96}}' | sort | uniq -c
   2352 1
   3631 3
     10 4
     50 5
   5401 NA

Is this expected?

No Exac scores for variants

Hello,

I have used 3 different softwares 1)Sniffles 2)npInv 3)NanoVar meant for calling structural variants from long read ONT data. I ran AnnotSV on the 3 VCFs separately but I don't get any Exac Scores.

Here is an excerpt from the input VCF:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  trimmed
chr1    350186  nv_SV18238-03RC4        N       <INV>   4.2     PASS    SVTYPE=INV;END=248942250;SVLEN=248592064;SR=2;NN=0.622  GT:DP:AD        1/1:2:0,2
chr1    475602  nv_SV10120-J3V6N        N       ]chr1:710590]N  2.6     PASS    SVTYPE=BND;END=.;SVLEN=.;SR=2;NN=0.448;SV2=TLO  GT:DP:AD        0/1:4:2,2
chr1    710580  nv_SV11577-6U3XJ        N       <INS>   6.9     PASS    SVTYPE=INS;END=710581;SVLEN=285;SR=3;NN=0.796   GT:DP:AD        1/1:3:0,3
chr1    710590  nv_SV10120-J3V6N        N       N[chr1:475602[  2.6     PASS    SVTYPE=BND;END=.;SVLEN=.;SR=2;NN=0.448;SV2=TLO  GT:DP:AD        0/1:4:2,2
chr1    908929  nv_SV18386-NW18S        N       <DEL>   4.4     PASS    SVTYPE=DEL;END=909323;SVLEN=-393;SR=2;NN=0.639  GT:DP:AD        1/1:2:0,2
chr1    1993702 nv_SV20252-FSNKQ        N       <DUP>   2.7     PASS    SVTYPE=DUP;END=1993884;SVLEN=182;SR=2;NN=0.462  GT:DP:AD        1/1:2:0,2
chr1    3016310 nv_SV8827-Q7X8T N       <DUP>   4.4     PASS    SVTYPE=DUP;END=3016710;SVLEN=400;SR=2;NN=0.637  GT:DP:AD        1/1:2:0,2
chr1    3016310 nv_SV8828-UPN0K N       <INS>   3.7     PASS    SVTYPE=INS;END=3016311;SVLEN=606;SR=2;NN=0.572  GT:DP:AD        0/1:3:1,2
chr1    3501983 nv_SV10305-3X4TN        N       <DUP>   4.0     PASS    SVTYPE=DUP;END=3502114;SVLEN=131;SR=2;NN=0.601  GT:DP:AD        1/1:2:0,2
chr1    5744253 nv_SV5610-VA01T N       <DEL>   4.2     PASS    SVTYPE=DEL;END=5744339;SVLEN=-85;SR=2;NN=0.621  GT:DP:AD        1/1:2:0,2
chr1    5829532 nv_SV2220-FJ586 N       <DUP>   4.3     PASS    SVTYPE=DUP;END=5829892;SVLEN=360;SR=2;NN=0.628  GT:DP:AD        1/1:2:0,2
chr1    5832242 nv_SV4441-6YFV5 N       <DUP>   4.6     PASS    SVTYPE=DUP;END=5832361;SVLEN=119;SR=3;NN=0.656  GT:DP:AD        1/1:3:0,3
chr1    5832242 nv_SV4442-73UDQ N       <INS>   4.3     PASS    SVTYPE=INS;END=5832243;SVLEN=664;SR=2;NN=0.625  GT:DP:AD        1/1:2:0,2
chr1    6005251 nv_SV2751-ZPY9B N       <DEL>   4.3     PASS    SVTYPE=DEL;END=6005465;SVLEN=-213;SR=2;NN=0.63  GT:DP:AD        1/1:2:0,2
chr1    6005881 nv_SV2749-0N9U4 N       <DEL>   4.3     PASS    SVTYPE=DEL;END=6006360;SVLEN=-478;SR=2;NN=0.63  GT:DP:AD        1/1:2:0,2
chr1    8500611 nv_SV5809-TI1KZ N       <DUP>   4.5     PASS    SVTYPE=DUP;END=8501174;SVLEN=563;SR=2;NN=0.644  GT:DP:AD        1/1:2:0,2

Here is an excerpt from the output from AnnotSV:

1_350186_248942250_INV  1       350186  248942250       248592064       INV     nv_SV18238-03RC4        N       <INV>   4.2     PASS    SVTYPE=INV;END=248942250;SVLEN=248592064;SR=2;NN=0.622  GT:DP:AD        1/1:2:0,2
       split   A3GALT2 NM_001080438    1028    14334   txStart-txEnd   5'UTR-3'UTR     33306765        33321098                0       0       -1              0       0       -1              -1      -1      1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:32435084-34634925_INV 0.4698                                  
                                                                                                                                        61.43   2.27028092535663        1.75809197357458        3.6237402371872e-07     -2.62354415217069       0.668347390481294       -2.47162789907313                                               2
1_350186_248942250_INV  1       350186  248942250       248592064       INV     nv_SV18238-03RC4        N       <INV>   4.2     PASS    SVTYPE=INV;END=248942250;SVLEN=248592064;SR=2;NN=0.622  GT:DP:AD        1/1:2:0,2
       split   AADACL3 NM_001103170    1228    12652   txStart-txEnd   5'UTR-3'UTR     12716109        12728760                0       0       -1              0       0       -1              -1      -1      1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV   0.4698                                                                                                                                  
                                        92.94   0.0361612141503088      -0.109500896056784      0.000110836921442839    -0.0099947629380129     -2.53125239294469       -2.47162789907313                               
                2

I don't get any Exac scores, instead there is 0 and -1. Could you please let me know if this is something that is expected?

Thank you,
Asma

Too slow when installing human genome

Hi
Thanks for developing such an awesome tool, it brings so much convenience to my work. However when I tried to install AnnotSV on a HPC, where the internet connection is not so good, the "make PREFIX=. install-human-annotation" takes so much and always break up. I want to know if I can download the human genome on my PC and upload it to the HPC, then run "make PREFIX=. install-human-annotation" without downloading the genome.
Could you give some advice? Many thanks!

Yang

gnomAD GRCh38 BED files have an empty line on top

Dear AnnotSV developers,

Thank you for such a nice tool.

We had experienced an issue which caused bedtools error:

...annotation in progress (August 17 2020 - 13:27)
-- gnomADannotation --
bedtools intersect -sorted -a ./test.cnv.formatted.sorted.bed.users.sorted.bed -b /home/annotsv/installed/share/AnnotSV/Annotations_Human/SVincludedInFt/gnomAD/GRCh38/20200716_liftoverGRCh38_gnomAD_DUP_SV.sorted.bed -wa -wb > ./test.cnv.formatted.sorted.intersect.gnomAD-DUP
Error: Type checker found wrong number of fields while tokenizing data line.
Exit with error

It appears to be an empty line in gnomAD GRCh38 BED files, deleting the first line will make it work again.
No issue with GRCh37.

Will you double check the files on your side please?

Best wishes,
Fengyuan

Incorrect line in the end of file *.annotsv.tsv

Hello, @lgmgeo!
We have run AnnotSV after new commit and have seen the unnecessary line at the end of all output files *.annotsv.tsv

Can you help to solve this problem?

-annotationsDir flag & manually update of Exomiser

Hello.

We are trying to use external reference directories for your tool (we are using Docker for tools and we down want to store 20GB reference in it), tool have support for it - -annotationsDir flag.
But for now all annotations are stored in one place - both own AnnotSV and Exomiser (for us).
Problem will emerge in future AnnotSV release - for now (2.3.2 AnnotSV) annotations are stored in 2.3.2/Annotations_Human and 2.3.2/Annotations_Exomiser/1902/1902_hg19.
Exomiser update will not cause problem: 2.3.2/Annotations_Exomiser/2003/2003_hg19.
AnnotSV version update will cause all other annotations to be placed into directories like 2.3.3/Annotations_Exomiser/2003/2003_hg19 for example, but files can be unchanged.

Implementing 2.3.2 directory (or something pointing current release version) into Annotations_Human will fix this problem.

Split annotation doesn't list genes found in deletions

Hello,

I am using AnnotSV in our workflow and I am impressed by its comprehensiveness. However, we found an issue regarding the annotation of genes found in deletions.

Each SV is first annotated as a whole (the "full" annotation type), with a column listing the affected genes that spans the two breakpoints. This method makes sense for duplication, inversion and translocation, but not for deletions because a deletion affects all the genes that it spans in addition to genes spanning its two breakpoints. For example, annotation of a DEL chr9:21850000-22100000 should list CDKN2A in addition to MTAP and CDKN2B-AS1 (two genes spanning the breakpoints), and all three genes should be annotated in "split". Therefore, it would be helpful if you could add this functionality to the pipeline.

Thank you so much for developing this very useful tool!

Best,
Joe

Seeking clarity on the Annotation code/Method

Hello Veronique,

Hope you are doing great out there.

I have a strange observation for a variant.
Coordinates : 1_108190708_108194629_DEL_1
Length : -3921bp
It's a Homozygous deletion in my VCF, covering 1st exon of 2nd transcript isoform for the gene SLC25A24 gene. As per the ACMG annotation via AnnotSV, it gets a criteria of 1A;2C-1 (SLC25A24);3A (1 gene);5F and a Likely pathogenic classification (Full = 4)

But, the similar deletion have been reported as Benign:

Source : 1000g;DDD:2369;IMH;dgv59e199;esv3587125;gnomAD-SV_v2.1_DEL_1_6945
Coordinates : 1:108189691-108195753;1:108190666-108194615;1:108190666-108194615;1:108190702-108194629;1:108190703-108194629;1:108190703-108194646

So, i am having doubt that it should be assigned 2F under Section 2 and a clear benign classification at the end.

Will you please look into this and update accordingly.

Thanks in Advance.

AnnotSV 2.4 Critical Bug (with GRCh38)

Dear AnnotSV users,

A critical bug has been identified when using AnnotSV 2.4 only with the GRCh38 genome Build. This impacts the DGV dataset and the ranking.

I am actively working on it and a new release should be delivered as soon as possible.

Sorry for any inconvenience this critical bug might have caused,

Best regards,

Véronique

Failed to download the data source from ENSEMBL (hg38)

Dear Igmgeo,
i tried downloading hg38 annotations, following things popped up:
downloading this:
wget ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.100.gtf.gz
did not work

what worked instead was manaual download from ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens (100->102) . then renamed the file.

Map BEDPE-based structrure variation (SV) to human genes (BED or GTF)?

Hi Geoffroy,

Does the latest AnnotSV support to map BEDPE-based structrure variation (SV) to human genes (BED or GTF)?

Thanks.

Shicheng

Problem installation AnnotSV 2.2

NOTE: This is NOT a replicate of #7

Hi @lgmgeo

I know that a new version of AnnotSV is already out (2.3) but for the purpose of testing our workflow, we want to stick to v2.2

I downloaded v2.2 from here
Unzipped that folder AnnotSV_2.2.tar.gz
Inside the folder, I ran this command
make PREFIX=.install

And I am seeing this issue

setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Configfile configuration
setenv: Variable name must contain alphanumeric characters.
------------------------
install -d .install/etc/AnnotSV
setenv: Variable name must contain alphanumeric characters.
install -p -m 0755 etc/AnnotSV/configfile  .install/etc/AnnotSV
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Executable installation
setenv: Variable name must contain alphanumeric characters.
-----------------------
install -d .install/bin/AnnotSV
setenv: Variable name must contain alphanumeric characters.
install -p -m 0755 bin/AnnotSV/AnnotSV.tcl .install/bin/AnnotSV
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Tcl scripts installation
setenv: Variable name must contain alphanumeric characters.
------------------------
install -d .install/share/tcl8.6/AnnotSV
setenv: Variable name must contain alphanumeric characters.
install -p -m 0644  share/tcl/AnnotSV/AnnotSV-extann.tcl share/tcl/AnnotSV/AnnotSV-exac.tcl share/tcl/AnnotSV/AnnotSV-filteredVCF.tcl share/tcl/AnnotSV/AnnotSV-write.tcl share/tcl/AnnotSV/AnnotSV-omim.tcl share/tcl/AnnotSV/AnnotSV-genehancer.tcl share/tcl/AnnotSV/AnnotSV-userBED.tcl share/tcl/AnnotSV/AnnotSV-gnomad.tcl share/tcl/AnnotSV/AnnotSV-config.tcl share/tcl/AnnotSV/AnnotSV-clingen.tcl share/tcl/AnnotSV/AnnotSV-vcf.tcl share/tcl/AnnotSV/AnnotSV-dgv.tcl share/tcl/AnnotSV/AnnotSV-repeat.tcl share/tcl/AnnotSV/AnnotSV-ranking.tcl share/tcl/AnnotSV/AnnotSV-refGene.tcl share/tcl/AnnotSV/AnnotSV-pathogenic-NR-SV.tcl share/tcl/AnnotSV/AnnotSV-ddd.tcl share/tcl/AnnotSV/AnnotSV-help.tcl share/tcl/AnnotSV/AnnotSV-gccontent.tcl share/tcl/AnnotSV/AnnotSV-general.tcl share/tcl/AnnotSV/AnnotSV-haploinsufficiency.tcl share/tcl/AnnotSV/AnnotSV-promoter.tcl share/tcl/AnnotSV/AnnotSV-1000g.tcl share/tcl/AnnotSV/AnnotSV-imh.tcl share/tcl/AnnotSV/AnnotSV-tad.tcl .install/share/tcl8.6/AnnotSV
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Documentations installation
setenv: Variable name must contain alphanumeric characters.
---------------------------
install -d .install/share/doc/AnnotSV
setenv: Variable name must contain alphanumeric characters.
install -p -m 0644  License.txt changeLog.txt commandLineOptions.txt README.AnnotSV_2.2.pdf .install/share/doc/AnnotSV
setenv: Variable name must contain alphanumeric characters.
/bin/cp -r share/doc/AnnotSV/Annotations_Human .install/share/doc/AnnotSV
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Installation of AnnotSV-2.2:
setenv: Variable name must contain alphanumeric characters.
--------------------------------
setenv: Variable name must contain alphanumeric characters.
DESTDIR=
setenv: Variable name must contain alphanumeric characters.
PREFIX=.install
setenv: Variable name must contain alphanumeric characters.
TCLVERSION=tcl8.6
setenv: Variable name must contain alphanumeric characters.

setenv: Variable name must contain alphanumeric characters.
Done

Kindly help

installation error

Hi there,
I just download the master file and unzip it. But when I run make to install it, it showed error message :'make: *** No rule to make target README.AnnotSV_2.3.pdf', needed by install-doc'. Stop.'. Cloud you help to resolve it? Thanks a lot.
Jian

AnnotSV implementation in Python

Hi users,

I'm wondering if anyone might be interested to implement AnnotSV in Python?
Then our users community could easily contribute towards it:

Bugs could be tackled efficiently
New ideas could be investigated faster

I look forward to the possibility of working together,
Hope someone might be interested in this nice and collaborative work.

Véronique
PS: The AnnotSV Source code is and will remain available under the GNU GPL licence

Issue about using GRCh38 and Exomiser

Hi,
I'm trying to use your software. But I found that the database was downloading while I was installing the software. However, I want to handle some SVs in hg38. The database downloaded by your software is like hg19.
There are only hg19 in the pic. So is the hg38 annotations here? Or which parameter should I set to have a hg38 annotation?

Thanks for your help!

No releases available - Exomiser update

There is a recent commit with commit message "New official release: 2.4", but there are no releases:
https://github.com/lgmgeo/AnnotSV/releases
Could you please hit the "Draft a new release" button to create a properly tagged release?

Suggestion for improvement: add options for user to define path to Annotation files

In order for AnnotSV to work in a docker containers, users need to download source code and annotation files(1000g etc.) inside the container. Because annotation files are quite big, the huge size of the image makes code improvement cycle slow and difficult.

One solution to this is allow users to download annotation file once, and pass the directory to AnnotSV at run time. I added an option -annotationfolder in my folk (zhouyangyu@9389022). I wish you could also add this options in your repo.

Cheers,
Joe

Tmp file not found while sorting cnv.bed

Dear developers,

Thanks for the latest release 2.5.1. I'm testing this version with my cnv calls (in BED format). Here is my command:

$ANNOTSV/bin/AnnotSV -SVinputFile 141.cnv.bed -snvIndelFiles 141.hard-filtered.vcf.gz -outputFile ./141.cnv.with-vcf.annotated.tsv -genomeBuild GRCh38 -svtBEDcol 6

Then I got an error:

sort -k1,1 -k2,2n ./141.cnv.formatted.sorted.bed.tmp >> ./141.cnv.formatted.sorted.bed
sort: cannot read: ./141.cnv.formatted.sorted.bed.tmp: No such file or directory
Exit with error

I don't see 141.cnv.formatted.sorted.bed.tmp in my working directory.

I tested it with a vcf as input file, and it works just fine.

Would you please advise what might cause the issue?

AnnotSV complains about sorting error (bedtools)

Hello,

I've encountered an issue, and I'm not sure the exact reason for it. I have an SV bed generated from an SV vcf.

The command I am using is:
"AnnotSV -SVinputFile all_sv.bed -SVinputInfo 1 -outputFile all_sv.bed.annotated.tsv

I encounter an error when the file is being annotated:

/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin/bedtools intersect -sorted -a ./all_sv.formatted.sorted.bed.users.sorted.bed -b /home/mcouse/AnnotSV_2.1/Annotations/SVincludedInFt/DDD/GRCh37/20190318_DDD_population_cnv.sorted.bed -wa -wb > ./all_sv.formatted.sorted.intersect.ddd Error: Sorted input specified, but the file ./all_sv.formatted.sorted.bed.users.sorted.bed has the following out of order record M 987 1611

In all_sv.formatted.sorted.bed.users.sorted.bed, I see:

M 987 1603
M 987 1611

There is only one SV in the original bed that corresponds to chromosome M and start position 987 (variant M 987 1611). I suspect this may be related to the refgene annotation, as the variant intersects with RNR1:

M 649 1603 + RNR1 NR_137294 1603 1603 649, 1603

Any thoughts on how this might be fixed?

Thanks for your help!

max size for a Tcl value (2147483647 bytes) exceeded

I'm running v2.2 of AnnotSV on a SGE cluster. I'm running on a couple of gene lists separately using "-candidateGenesFile" and "-candidateGenesFiltering". The run completes for a small gene list, but fails for the larger gene list and exits abruptly. The error message is in the subject line. I tried giving more memory to the job (200G), but that doesn't fix it as there doesn't seem to be a way to specify to AnnotSV (or Tcl) to use more memory. I'm going to try splitting my gene list into two and see if that works. Is there another fix for this?

Thanks,
Eric

Issue with mouse-annotation

Hello,

I got an issue with (make PREFIX=. install-mouse-annotation) it seems that the file Annotations Mouse 2.3.2.tar.gz does not exist.

make PREFIX=. install-mouse-annotation

Installation of mouse annotation:

install -d ./share/AnnotSV/
tar -xf Annotations_Mouse_2.3.2.tar.gz -C ./share/AnnotSV/
tar: This does not look like a tar archive

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Makefile:164: recipe for target 'install-mouse-annotation' failed
make: *** [install-mouse-annotation] Error 2

Thanks,

dbVAR's Clinical SV & NCBI Curated Common SV

Are those db from dbVar included in AnnotSV?

Clinical SV
https://www.ncbi.nlm.nih.gov/dbvar/content/clinvar_summary

NCBI Curated Common SV
https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/

Thanks!

Annot-SV 2.3.2 crashes in the running exomiser step

Hi , Im trying to run the latest annot-sv with HPO terms and it crashes as it can't find json package. Would be great if you can help. I've pasted the error below.
..running Exomiser
can't find package json 1.3.3
while executing
"package require json 1.3.3"
(procedure "runExomiser" line 9)
invoked from within
"runExomiser "$L_allGenesOverlapped" "$g_AnnotSV(hpo)""
(procedure "refGeneAnnotation" line 262)
invoked from within
"refGeneAnnotation"

Thanks,
Archana

lines containing only "full" (with AnnotSV v2.0)

hi, I'm running v2.0 of AnnotSV on a SGE cluster. There are many lines containing only "full" in my output, but I don't know how to deal with it.

install problem

I follow these instructions:

cd /path/to/install/
git clone https://github.com/lgmgeo/AnnotSV.git
make PREFIX=. install
and download 3 database using Axel
2007_hg19.tar.gz
2007_phenotype.zip
Annotations_Human_3.0.7.tar.gz
make PREFIX=. install-human-annotation

error occured:

Installation of Exomiser data:

install -d -p ./share/AnnotSV/Annotations_Exomiser/2007
tar -xf 2007_hg19.tar.gz -C ./share/AnnotSV/Annotations_Exomiser/2007/
unzip 2007_phenotype.zip -d ./share/AnnotSV/Annotations_Exomiser/2007/
Archive: 2007_phenotype.zip
skipping: 2007_phenotype/2007_phenotype.h2.db need PK compat. v4.5 (can do v2.1)
creating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/rw_string_10.mv
creating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/
creating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/4.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/10.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/20.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/17_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/3_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/15.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/11.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/4_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/16.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/5_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/12.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/12_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/17.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/13.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/11_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/15_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/14_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/16_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/18.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/7_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/14.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/10_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/3.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/19.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/18_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/2.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/9_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/9.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/1.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/20_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/8.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/7.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/2_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/6_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/13_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/6.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/8_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/1_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/19_symmetric.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/out/5.out
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/hp.obo
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype/phenix/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
inflating: ./share/AnnotSV/Annotations_Exomiser/2007/2007_phenotype.sha256
make: *** [Makefile:150: install-exomiser-1] Error 81

could you please be so kind to help me with this error?
Thank you so so so much!

bedtools in v3.0.7 not found

Hi,
I am sorry to bother you, but i have the question, when I update my annotSV to the 3.0.7, it gives me an error with the same code. Can you give me some advice?

#AnnotSV_2.3 works well :

export PATH=$PATH:~/BEDTOOLS/bedtools-2.25.0/bin/
export ANNOTSV=~/SVtools/AnnotSV_2.3/

~/SVtools/AnnotSV_2.3/bin/AnnotSV \
-bedtools ~/BEDTOOLS/bedtools-2.25.0/bin/bedtools \
-SVinputFile annovar.hg19_multianno.vcf \
-outputFile ./anno.vcf \
-outputDir . \
-overwrite yes

#AnnotSV_3.0.7 error:

export PATH=$PATH:~/BEDTOOLS/bedtools-2.25.0/bin/
export ANNOTSV=~/SVtools/AnnotSV_3.0.7/AnnotSV-master/
~/SVtools/AnnotSV_3.0.7/AnnotSV-master/bin/AnnotSV \
-bedtools ~/BEDTOOLS/bedtools-2.25.0/bin/bedtools \
-SVinputFile annovar.hg19_multianno.vcf \
-outputFile ./anno.vcf \
-outputDir . \
-overwrite yes

#output 
...

/AnnotSV/configfile
	...configuration data given in arguments
	...checking all these configuration data

############################################################################
############################################################################
Bad value for the bcftools option (bcftools)
couldn't execute "bcftools": no such file or directory
Exit with error.
############################################################################

Thank you.
Xiucz

New look for AnnotSV online results

Dear AnnotSV users,

Today, we are very happy to announce that the "AnnotSV 3.0 online results" will be now displayed using the knotAnnotSV program.
This software is developed in collaboration with Thomas Guignard (CHU Montpellier, France) and can be accessed together with its documentation using the following links:
https://github.com/mobidic/knotAnnotSV

We hope that you will find this new display useful and please do not hesitate to give feedback using the following emails:
[email protected]

Happy exploring,

Véronique and Thomas

Add column for frequencies in databases for B_* infos (and eventually for P_*)

Would it be possible to include in annotated results frequencies from SV databases? It would help to better assess some events.

Thanks for your help and for your useful software.

pLI for SVs

Mixed columns in results (depending on the machines)

Hello again.
We start testing annotsv and found some inconsistency - column names and content is mixed. Ar far as I can see content is same, it is just mixed.
Runs were same but on different machines - maybe this order is pseudo random and machine dependent,
Upper part of first file:

AnnotSV ID	SV chrom	SV start	SV end	SV length	SV type	ID	REF	ALT	QUAL	FILTER	INFO	AnnotSV type	Gene name	NM	CDS length	tx length	location	location2	intersectStart	intersectEnd	DGV_GAIN_IDs	DGV_GAIN_n_samples_with_SV	DGV_GAIN_n_samples_tested	DGV_GAIN_Frequency	DGV_LOSS_IDs	DGV_LOSS_n_samples_with_SV	DGV_LOSS_n_samples_tested	DGV_LOSS_Frequency	GD_ID	GD_AN	GD_N_HET	GD_N_HOMALT	GD_AF	GD_POPMAX_AF	GD_ID_others	1000g_event	1000g_AF	1000g_max_AF	IMH_ID	IMH_AF	IMH_ID_others	promoters	dbVar_event	dbVar_variant	dbVar_status	TADcoordinates	ENCODEexperiments	GCcontent_left	GCcontent_right	Repeats_coord_left	Repeats_type_left	Repeats_coord_right	Repeats_type_right	ACMG	delZ_ExAC	dupZ_ExAC	cnvZ_ExAC	synZ_ExAC	misZ_ExAC	pLI_ExAC	HI_CGscore	TriS_CGscore	HI_DDDpercent	DDD_status	DDD_mode	DDD_consequence	DDD_disease	DDD_pmids	Phenotypes	Inheritance	morbidGenes	morbidGenesCandidates	Mim Number	AnnotSV ranking
1_633720_633721_BND_1	1	633720	633721		BND	MantaBND:3:0:1:0:0:0:1	T	T]chr8:62102872]	.	.	SVTYPE=BND;MATEID=MantaBND:3:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=TC;BND_PAIR_COUNT=6;PAIR_COUNT=6	full									gssvG11,gssvG4,gssvG38,gssvG84	34	19719	0.00172423	gssvL13,gssvL7,gssvL32,gssvL38	22	8400	0.00261905					-1	-1	gnomAD_v2_DUP_1_23;gnomAD_v2_DEL_1_27		-1	-1		-1	1:83945-209460925_INV							0.420	0.420																									2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	full	A3GALT2/AADACL3/AADACL4/ABCA4/ABCD3/ABL2/ACADM/ACAP3/ACBD6/ACKR1/ACOT11/ACOT7/ACP6/ACTG1P20/ACTG1P4/ACTL8/ACTRT2/ADAM15/ADAM30/ADAMTS4/ADAMTSL4/ADAMTSL4-AS1/ADAR/ADCY10/ADGRB2/ADGRL2/ADGRL4/ADIPOR1/ADORA1/ADORA3/ADPRHL2/AGBL4/AGBL4-AS1/AGBL4-IT1/AGL/AGMAT/AGO1/AGO3/AGO4/AGRN/AGTRAP/AHCYL1/AHDC1/AIDA/AIM2/AJAP1/AK2/AK4/AK5/AKIRIN1/AKNAD1/AKR1A1/AKR7A2/AKR7A2P1/AKR7A3/AKR7L/ALDH4A1/ALDH9A1/ALG14/ALG14-AS1/ALG6/ALPL/ALX3/AMIGO1/AMPD1/AMPD2/AMY1A/AMY1B/AMY1C/AMY2A/AMY2B/ANGEL2/ANGPTL1/ANGPTL3/ANGPTL7/ANKRD13C/ANKRD34A/ANKRD35/ANKRD36BP1/ANKRD45/ANKRD65/ANP32E/ANXA9/AP4B1/AP4B1-AS1/APCS/APH1A/APOA2/APOBEC4/AQP10/ARHGAP29/ARHGAP30/ARHGEF10L/ARHGEF11/ARHGEF16/ARHGEF19/ARHGEF2/ARID1A/ARL8A/ARMH1/ARNT/ARPC5/ARTN/ASAP3/ASB17/ASCL5/ASH1L/ASH1L-AS1/ASPM/ASTN1/ATAD3A/ATAD3B/ATAD3C/ATF3/ATF6/ATG4C/ATP13A2/ATP1A1/ATP1A1-AS1/ATP1A2/ATP1A4/ATP1B1/ATP2B4/ATP5IF1/ATP5PB/ATP6V0B/ATP6V1G3/ATP8B2/ATPAF1/ATXN7L2/AUNIP/AURKAIP1/AURKAP1/AVPR1B/AXDND1/AZIN2/B3GALT2/B3GALT6/B4GALT2/B4GALT3/BARHL2/BATF3/BCAN/BCAR3/BCAR3-AS1/BCAS2/BCL10/BCL2L15/BCL9/BEND5/BEST4/BGLAP/BLACAT1/BLZF1/BMP8A/BMP8B/BNIPL/BOLA1/BPNT1/BRDT/BRINP2/BRINP3/BROX/BSDC1/BSND/BTBD19/BTBD8/BTF3L4/BTG2/C1QA/C1QB/C1QC/C1QTNF12/C1orf105/C1orf109/C1orf112/C1orf115/C1orf116/C1orf122/C1orf127/C1orf137/C1orf140/C1orf141/C1orf143/C1orf146/C1orf158/C1orf159/C1orf162/C1orf167/C1orf167-AS1/C1orf174/C1orf185/C1orf189/C1orf194/C1orf195/C1orf21/C1orf210/C1orf216/C1orf220/C1orf226/C1orf232/C1orf43/C1orf50/C1orf52/C1orf53/C1orf54/C1orf56/C1orf61/C1orf68/C1orf74/C1orf87/C1orf94/C2CD4D/C2CD4D-AS1/C4BPA/C4BPB/C8A/C8B/CA14/CA6/CACHD1/CACNA1E/CACNA1S/CACYBP/CADM3/CADM3-AS1/CALML6/CALR4P/CAMK1G/CAMK2N1/CAMSAP2/CAMTA1/CAMTA1-AS2/CAMTA1-DT/CAP1/CAPN2/CAPN8/CAPZA1/CAPZB/CASP9/CASQ1/CASQ2/CASZ1/CATSPER4/CC2D1B/CCDC163/CCDC17/CCDC18/CCDC18-AS1/CCDC181/CCDC185/CCDC190/CCDC24/CCDC27/CCDC28B/CCDC30/CCN1/CCNL2/CCT3/CD101/CD160/CD164L2/CD1A/CD1B/CD1C/CD1D/CD1E/CD2/CD244/CD247/CD34/CD46/CD48/CD52/CD53/CD55/CD58/CD5L/CD84/CDA/CDC14A/CDC20/CDC42/CDC42SE1/CDC7/CDC73/CDCA8/CDCP2/CDK11A/CDK11B/CDK18/CDKN2C/CELA2A/CELA2B/CELA3A/CELA3B/CELF3/CELSR2/CENPF/CENPL/CENPS/CENPS-CORT/CEP104/CEP350/CEP85/CEPT1/CERS2/CFAP126/CFAP45/CFAP57/CFAP74/CFH/CFHR1/CFHR2/CFHR3/CFHR4/CFHR5/CGN/CHD1L/CHD5/CHI3L1/CHI3L2/CHIA/CHIAP2/CHIT1/CHRNB2/CHTOP/CIART/CITED4/CKS1B/CLCA1/CLCA2/CLCA3P/CLCA4/CLCA4-AS1/CLCC1/CLCN6/CLCNKA/CLCNKB/CLDN19/CLIC4/CLK2/CLSPN/CLSTN1/CMPK1/CNKSR1/CNN3/CNR2/CNTN2/COA7/COL11A1/COL16A1/COL24A1/COL8A2/COL9A2/COLGALT2/COP1/COPA/CORT/CPLANE2/CPT2/CPTP/CR1/CR1L/CR2/CRABP2/CRB1/CRCT1/CREB3L4/CREG1/CRNN/CROCC/CROCCP2/CROCCP3/CRP/CRTC2/CRYBG2/CRYZ/CRYZL2P/CRYZL2P-SEC16B/CSDE1/CSF1/CSF3R/CSMD2/CSMD2-AS1/CSRP1/CTBS/CTH/CTNNBIP1/CTPS1/CTRC/CTSE/CTSK/CTSS/CTTNBP2NL/CTXND2/CYB561D1/CYB5R1/CYB5RL/CYCSP52/CYMP/CYMP-AS1/CYP2J2/CYP4A11/CYP4A22/CYP4B1/CYP4X1/CYP4Z1/CYP4Z2P/CZIB/DAB1/DAB1-AS1/DAP3/DARS2/DBT/DCAF6/DCAF8/DCDC2B/DCLRE1B/DCST1/DCST1-AS1/DCST2/DDAH1/DDI2/DDOST/DDR2/DDX20/DDX59/DDX59-AS1/DEDD/DENND1B/DENND2C/DENND2D/DENND4B/DEPDC1/DEPDC1-AS1/DFFA/DFFB/DHCR24/DHDDS/DHDDS-AS1/DHRS3/DHX9/DIO1/DIPK1A/DIRAS3/DISP1/DISP3/DLEU2L/DLGAP3/DLSTP1/DMAP1/DMBX1/DMRTA2/DMRTB1/DNAJA1P5/DNAJB4/DNAJC11/DNAJC16/DNAJC6/DNAJC8/DNALI1/DNASE2B/DNM3/DNM3-IT1/DNM3OS/DNTTIP2/DOCK7/DPH2/DPH5/DPM3/DPT/DPYD/DPYD-AS1/DPYD-AS2/DR1/DRAM2/DRAXIN/DRD5P2/DSTYK/DTL/DUSP10/DUSP12/DUSP23/DUSP27/DVL1/DYRK3/E2F2/EBNA1BP2/ECE1/ECE1-AS1/ECHDC2/ECM1/EDEM3/EDN2/EEF1AKNMT/EFCAB14/EFCAB14-AS1/EFCAB7/EFHD2/EFNA1/EFNA3/EFNA4/EIF2B3/EIF2D/EIF3I/EIF4G3/ELAVL4/ELF3/ELF3-AS1/ELK4/ELOA/ELOA-AS1/ELOVL1/EMBP1/EMC1/EMC1-AS1/ENO1/ENO1-AS1/ENSA/EPB41/EPHA10/EPHA2/EPHA8/EPHB2/EPHX4/EPRS1/EPS15/EPS8L3/ERI3/ERI3-IT1/ERICH3/ERICH3-AS1/ERLNC1/ERMAP/ERRFI1/ESPN/ESPNP/ESRRG/ETNK2/ETV3/ETV3L/EVA1B/EVI5/EXO5/EXOSC10/EXOSC10-AS1/EXTL1/EXTL2/EYA3/F11R/F13B/F3/F5/FAAH/FAAHP1/FAAP20/FABP3/FAF1/FALEC/FAM102B/FAM110D/FAM131C/FAM151A/FAM163A/FAM167B/FAM177B/FAM183A/FAM189B/FAM20B/FAM229A/FAM41C/FAM43B/FAM71A/FAM72A/FAM72B/FAM72C/FAM72D/FAM76A/FAM78B/FAM87B/FASLG/FBLIM1/FBXO2/FBXO42/FBXO44/FBXO6/FCAMR/FCER1A/FCER1G/FCGR1A/FCGR1B/FCGR1CP/FCGR2A/FCGR2B/FCGR2C/FCGR3A/FCGR3B/FCMR/FCN3/FCRL1/FCRL2/FCRL3/FCRL4/FCRL5/FCRL6/FCRLA/FCRLB/FDPS/FGGY/FGR/FHAD1/FHAD1-AS1/FHL3/FLAD1/FLG/FLG-AS1/FLG2/FLJ37453/FLVCR1/FLVCR1-DT/FMO1/FMO2/FMO3/FMO4/FMO5/FMO6P/FMO9P/FMOD/FNBP1L/FNDC10/FNDC5/FNDC7/FOXD2/FOXD2-AS1/FOXD3/FOXD3-AS1/FOXE3/FOXJ3/FOXO6/FOXO6-AS1/FPGT/FPGT-TNNI3K/FRRS1/FUBP1/FUCA1/FYB2/G0S2/GABPB2/GABRD/GADD45A/GALE/GAS5/GAS5-AS1/GATAD2B/GBA/GBAP1/GBAT2/GBP1/GBP1P1/GBP2/GBP3/GBP4/GBP5/GBP6/GBP7/GCLM/GDAP2/GEMIN8P4/GFI1/GIPC2/GJA4/GJA5/GJA8/GJA9/GJA9-MYCBP/GJB3/GJB4/GJB5/GLIS1/GLMN/GLMP/GLRX2/GLUL/GMEB1/GNAI3/GNAT2/GNB1/GNG12/GNG12-AS1/GNG5/GNL2/GNRHR2/GOLPH3L/GOLT1A/GON4L/GORAB/GORAB-AS1/GPA33/GPATCH2/GPATCH3/GPATCH4/GPBP1L1/GPN2/GPR153/GPR157/GPR161/GPR25/GPR3/GPR37L1/GPR52/GPR61/GPR88/GPR89A/GPR89B/GPSM2/GPX7/GRHL3/GRIK3/GS1-279B7.1/GSTM1/GSTM2/GSTM3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11/SRSF4/SSBP3/SSBP3-AS1/SSR2/SSU72/SSX2IP/ST3GAL3/ST6GALNAC3/ST6GALNAC5/ST7L/STIL/STK40/STMN1/STPG1/STRIP1/STX12/STX6/STXBP3/SUCO/SUMO1P3/SUSD4/SV2A/SVBP/SWT1/SYCP1/SYDE2/SYF2/SYNC/SYPL2/SYT11/SYT14/SYT2/SYT6/SYTL1/SZRD1/SZT2/SZT2-AS1/TACSTD2/TADA1/TAF12/TAF13/TAF1A/TAF1A-AS1/TAFA3/TAGLN2/TAL1/TARDBP/TARS2/TAS1R1/TAS1R2/TAS1R3/TATDN3/TBX15/TBX19/TCEA3/TCEANC2/TCHH/TCHHL1/TCTEX1D1/TCTEX1D4/TDRD10/TDRD5/TDRKH/TDRKH-AS1/TEDDM1/TEKT2/TENT5B/TENT5C/TESK2/TEX35/TEX38/TEX46/TEX50/TFAP2E/TGFB2/TGFB2-AS1/TGFB2-OT1/TGFBR3/THAP3/THBS3/THEM4/THEM5/THEMIS2/THRAP3/TIE1/TIMM17A/TINAGL1/TIPRL/TLCD4/TLCD4-RWDD3/TLR5/TM2D1/TMCC2/TMCO1/TMCO1-AS1/TMCO2/TMCO4/TMED5/TMEM125/TMEM167B/TMEM183A/TMEM200B/TMEM201/TMEM222/TMEM234/TMEM240/TMEM269/TMEM269-DT/TMEM274P/TMEM275/TMEM35B/TMEM39B/TMEM50A/TMEM51/TMEM51-AS1/TMEM52/TMEM53/TMEM54/TMEM59/TMEM61/TMEM69/TMEM79/TMEM81/TMEM82/TMEM88B/TMEM9/TMIGD3/TMOD4/TNFAIP8L2/TNFAIP8L2-SCNM1/TNFRSF14/TNFRSF14-AS1/TNFRSF18/TNFRSF1B/TNFRSF25/TNFRSF4/TNFRSF8/TNFRSF9/TNFSF18/TNFSF4/TNN/TNNI1/TNNI3K/TNNT2/TNR/TOE1/TOMM40L/TOP1P1/TOR1AIP1/TOR1AIP2/TOR3A/TP53BP2/TP73/TP73-AS1/TPM3/TPR/TPRG1L/TRABD2B/TRAF3IP3/TRAF5/TRAPPC3/TRIM33/TRIM45/TRIM46/TRIM62/TRIM63/TRIT1/TRMT13/TRMT1L/TRNAU1AP/TRNP1/TSACC/TSEN15/TSHB/TSPAN1/TSPAN2/TSSK3/TSTD1/TTC22/TTC24/TTC34/TTC39A/TTC39A-AS1/TTC4/TTF2/TTLL10/TTLL7/TUFT1/TUT4/TXLNA/TXNDC12/TXNDC12-AS1/TXNIP/TYW3/UAP1/UBAP2L/UBE2J2/UBE2Q1/UBE2Q1-AS1/UBE2T/UBE2U/UBE4B/UBIAD1/UBL4B/UBQLN4/UBR4/UBXN10/UBXN10-AS1/UBXN11/UCHL5/UCK2/UFC1/UHMK1/UOX/UQCRH/UQCRHL/UROD/USF1/USH2A/USP1/USP21/USP24/USP33/USP48/UTP11/UTP25/UTS2/VAMP3/VAMP4/VANGL1/VANGL2/VASH2/VAV3/VAV3-AS1/VCAM1/VHLL/VPS13D/VPS45/VPS72/VSIG8/VTCN1/VWA1/VWA5B1/WARS2/WARS2-AS1/WARS2-IT1/WASF2/WDR3/WDR47/WDR63/WDR77/WDR78/WDTC1/WLS/WNT2B/WNT4/WRAP73/XCL1/XCL2/XKR8/XPR1/YARS1/YBX1/YIPF1/YOD1/YRDC/YTHDF2/YY1AP1/ZBED6/ZBTB17/ZBTB37/ZBTB40/ZBTB41/ZBTB48/ZBTB7B/ZBTB8A/ZBTB8B/ZBTB8OS/ZC3H11A/ZC3H11B/ZC3H12A/ZCCHC17/ZDHHC18/ZFP69/ZFP69B/ZFYVE9/ZMPSTE24/ZMYM1/ZMYM4/ZMYM4-AS1/ZMYM6/ZMYND12/ZNF281/ZNF326/ZNF362/ZNF436/ZNF436-AS1/ZNF593/ZNF644/ZNF648/ZNF683/ZNF684/ZNF687/ZNF687-AS1/ZNF691/ZNF697/ZNHIT6/ZPLD2P/ZRANB2/ZRANB2-AS1/ZRANB2-AS2/ZSCAN20/ZSWIM5/ZYG11A/ZYG11B/ZZZ3	copy_number_gain;copy_number_loss;deletion;duplication	essv4368444;nssv1157165;nssv1157168;nssv1157189;nssv1157193;nssv1157214;nssv1157217;nssv1157250;nssv1157273;nssv1157274;nssv1157306;nssv1157307;nssv1157308;nssv1157309;nssv1157311;nssv1157315;nssv1157875;nssv13638693;nssv13638713;nssv13638840;nssv13638876;nssv13638979;nssv13638987;nssv13639292;nssv13639373;nssv13639487;nssv13639504;nssv13639620;nssv13639665;nssv13639713;nssv13640035;nssv13640262;nssv13640286;nssv13640404;nssv13640535;nssv13640569;nssv13640623;nssv13640672;nssv13640809;nssv13641138;nssv13641147;nssv13641189;nssv13641209;nssv13641247;nssv13641271;nssv13641324;nssv13641350;nssv13642021;nssv13642151;nssv13642154;nssv13642383;nssv13642390;nssv13642590;nssv13642778;nssv13643109;nssv13643277;nssv13643278;nssv13643714;nssv13643716;nssv13644070;nssv13644157;nssv13644718;nssv13644720;nssv13644784;nssv13644918;nssv13645225;nssv13645443;nssv13645530;nssv13646223;nssv13646455;nssv13646717;nssv13647205;nssv13647265;nssv13647315;nssv13647423;nssv13647497;nssv13647559;nssv13647615;nssv13648427;nssv13648455;nssv13648557;nssv13648612;nssv13648634;nssv13648744;nssv13648889;nssv13648971;nssv13649175;nssv13649365;nssv13649375;nssv13649432;nssv13649466;nssv13649968;nssv13649989;nssv13650373;nssv13650602;nssv13650648;nssv13650929;nssv13651000;nssv13651072;nssv13651277;nssv13651479;nssv13651574;nssv13651583;nssv13651645;nssv13651859;nssv13652057;nssv13652240;nssv13652345;nssv13652463;nssv13652903;nssv13653083;nssv13653093;nssv13653103;nssv13653129;nssv13653198;nssv13653218;nssv13653300;nssv13653365;nssv13653606;nssv13653667;nssv13653687;nssv13654185;nssv13654197;nssv13654255;nssv13654261;nssv13654326;nssv13654496;nssv13654536;nssv13654566;nssv13654929;nssv13654953;nssv13655057;nssv13655179;nssv13655235;nssv13655558;nssv13655807;nssv13656051;nssv13656120;nssv13656441;nssv13656517;nssv13656566;nssv14081994;nssv14081997;nssv14082061;nssv14082144;nssv14082163;nssv14082177;nssv14082244;nssv14082308;nssv14082318;nssv14082321;nssv14082355;nssv14082394;nssv14082395;nssv14082408;nssv14082499;nssv14082523;nssv1415016;nssv1415217;nssv1415280;nssv1415282;nssv1415285;nssv1415305;nssv1415327;nssv1415329;nssv1415401;nssv1415419;nssv1415490;nssv1415513;nssv1415519;nssv1494821;nssv1494822;nssv1494823;nssv1494824;nssv1494826;nssv1494827;nssv1494828;nssv1494829;nssv1494831;nssv1494832;nssv1494833;nssv1494834;nssv1494835;nssv1494836;nssv1494837;nssv1494838;nssv1494840;nssv1494841;nssv1494842;nssv1494843;nssv1494844;nssv1495166;nssv1495167;nssv1495168;nssv1495722;nssv15119723;nssv15119728;nssv15119731;nssv15119768;nssv15119931;nssv15119937;nssv15119938;nssv15119939;nssv15119944;nssv15120115;nssv15120130;nssv15120157;nssv15120191;nssv15120196;nssv15120201;nssv15120497;nssv15120751;nssv15120755;nssv15120756;nssv15121047;nssv15121050;nssv15121100;n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15770172;nssv15770192;nssv15770194;nssv15770215;nssv15770230;nssv15770284;nssv15770286;nssv15770324;nssv15770412;nssv15770418;nssv15770420;nssv15770429;nssv15770457;nssv15770522;nssv15770527;nssv15770533;nssv15770545;nssv15770606;nssv15770626;nssv15770645;nssv15770728;nssv15770744;nssv15770764;nssv15770765;nssv15770795;nssv15770850;nssv15770858;nssv15770860;nssv15770901;nssv15770973;nssv15770994;nssv15771000;nssv15771042;nssv15771044;nssv15771413;nssv15771414;nssv15771415;nssv15771416;nssv15771417;nssv15771418;nssv15771419;nssv15771460;nssv15771461;nssv15771469;nssv15771480;nssv15771484;nssv15771494;nssv15771498;nssv15771528;nssv15771586;nssv15771607;nssv15771652;nssv15771746;nssv15771750;nssv15771763;nssv15771771;nssv15771790;nssv15771818;nssv15772052;nssv15772355;nssv15772838;nssv15773206;nssv15773642;nssv15773680;nssv15773714;nssv15773719;nssv15773720;nssv15773733;nssv15773734;nssv15773735;nssv15773738;nssv15773765;nssv15773787;nssv15773788;nssv15773792;nssv15773818;nssv15773826;nssv15773849;nssv15773933;nssv15773952;nssv15773956;nssv15773962;nssv15774107;nssv15774128;nssv15774138;nssv15774159;nssv15774161;nssv15774344;nssv15774627;nssv15775494;nssv15775904;nssv15776177;nssv15776374;nssv15776405;nssv15776578;nssv15776768;nssv15776860;nssv15776866;nssv15776867;nssv15776877;nssv15776884;nssv15776888;nssv15776891;nssv15776892;nssv15776900;nssv15776903;nssv15776906;nssv15776916;nssv15776917;nssv15776928;nssv15776937;nssv15776942;nssv15777025;nssv15777031;nssv15777034;nssv15777043;nssv15777243;nssv15777298;nssv15777321;nssv15777369;nssv15777491;nssv15777494;nssv15777505;nssv15777538;nssv15777556;nssv15777589;nssv15777605;nssv15777609;nssv15777638;nssv15777646;nssv15777685;nssv15777715;nssv15777717;nssv15777730;nssv15777747;nssv15777764;nssv1601514;nssv1601722;nssv1601816;nssv1601987;nssv1602013;nssv1602095;nssv1602144;nssv1602148;nssv1602152;nssv1602217;nssv1602221;nssv1602225;nssv1602226;nssv1602228;nssv1602237;nssv1602242;nssv1602489;nssv1602495;nssv1602523;nssv1602734;nssv1602972;nssv1602989;nssv1602993;nssv1603181;nssv1603197;nssv1603536;nssv1603664;nssv1603787;nssv1603793;nssv1603980;nssv1604112;nssv1604129;nssv1604131;nssv1604136;nssv1604142;nssv1604154;nssv1604194;nssv1604364;nssv1604370;nssv1604393;nssv1604655;nssv1604674;nssv1604767;nssv1604929;nssv1607568;nssv1607648;nssv1608111;nssv1608112;nssv1608157;nssv1608159;nssv1608217;nssv1608266;nssv1608295;nssv1608846;nssv1608908;nssv1609140;nssv1609251;nssv1609366;nssv1609367;nssv1609369;nssv1609602;nssv1609603;nssv1610085;nssv1610100;nssv1610103;nssv1610127;nssv1610143;nssv1610261;nssv1610268;nssv1610367;nssv1610374;nssv1610405;nssv1610445;nssv1610446;nssv1610454;nssv1610460;nssv1610617;nssv1610683;nssv1610691;nssv1610695;nssv1610715;nssv1610742;nssv1610746;nssv1610798;nssv1610825;nssv1610911;nssv1610948;nssv1610998;nssv1611053;nssv1611070;nssv1611125;nssv1611163;nssv1611222;nssv1611228;nssv1611343;nssv1611363;nssv1611397;nssv1611471;nssv1611477;nssv1611482;nssv1611558;nssv1611567;nssv1611612;nssv1611625;nssv1611637;nssv1611666;nssv1611701;nssv1611725;nssv1611759;nssv1611802;nssv1611809;nssv1611841;nssv1611845;nssv1611862;nssv1611900;nssv1611901;nssv1611954;nssv1612001;nssv1612030;nssv1612055;nssv1612087;nssv1612097;nssv1612105;nssv1612117;nssv1612189;nssv1612197;nssv1612258;nssv1612290;nssv1612317;nssv1612321;nssv1612364;nssv1612388;nssv1612403;nssv1612433;nssv1612454;nssv1612458;nssv1612497;nssv1612506;nssv1612529;nssv1612536;nssv1612627;nssv1612653;nssv1612699;nssv1612753;nssv1612754;nssv1612815;nssv1612825;nssv1614058;nssv2767595;nssv3394988;nssv3395098;nssv3395100;nssv3395202;nssv3395279;nssv3395311;nssv3395459;nssv3395509;nssv3395745;nssv3395752;nssv3395783;nssv3395996;nssv3396032;nssv3396046;nssv3396064;nssv3396112;nssv3396128;nssv3396288;nssv3396309;nssv3396358;nssv3396378;nssv3396407;nssv3396408;nssv3396444;nssv3396454;nssv3396489;nssv3396509;nssv3396606;nssv3396607;nssv3396638;nssv3396640;nssv3396731;nssv3396744;nssv3396886;nssv3397008;nssv3397095;nssv3397132;nssv3397176;nssv3397270;nssv3397381;nssv3397436;nssv3443291;nssv3445546;nssv3445882;nssv3446048;nssv3447232;nssv3448513;nssv3450228;nssv3450308;nssv3452442;nssv3453616;nssv3454617;nssv3455079;nssv3456133;nssv3457122;nssv3457499;nssv3458389;nssv3459009;nssv3460391;nssv3462607;nssv3487351;nssv3497102;nssv3761542;nssv3761544;nssv3761549;nssv3761593;nssv3761620;nssv451365;nssv575269;nssv575320;nssv575321;nssv575399;nssv575445;nssv575446;nssv575447;nssv575658;nssv575679;nssv575720;nssv575740;nssv575864;nssv575868;nssv575896;nssv575948;nssv576063;nssv576149;nssv576212;nssv576287;nssv576295;nssv576300;nssv576309;nssv576311;nssv576338;nssv576345;nssv576346;nssv576394;nssv576459;nssv576468;nssv576489;nssv576618;nssv576639;nssv576645;nssv576927;nssv576931;nssv576933;nssv576934;nssv576935;nssv576936;nssv576938;nssv576939;nssv576940;nssv576941;nssv576942;nssv576945;nssv576946;nssv576947;nssv576949;nssv576952;nssv576954;nssv576955;nssv577125;nssv577127;nssv577128;nssv577129;nssv577130;nssv577131;nssv577133;nssv577134;nssv577135;nssv577136;nssv577138;nssv577139;nssv577140;nssv577141;nssv577142;nssv577143;nssv577144;nssv577150;nssv577152;nssv577154;nssv577155;nssv577156;nssv577157;nssv577158;nssv577160;nssv577161;nssv577162;nssv577164;nssv577165;nssv577166;nssv577167;nssv577168;nssv577171;nssv577174;nssv577176;nssv577179;nssv577180;nssv577183;nssv577184;nssv577185;nssv577186;nssv577187;nssv577188;nssv577189;nssv577190;nssv577191;nssv577194;nssv577196;nssv577197;nssv577198;nssv577199;nssv577200;nssv577201;nssv577202;nssv577204;nssv577205;nssv577206;nssv577207;nssv577208;nssv577209;nssv577210;nssv577211;nssv577212;nssv577216;nssv577217;nssv577218;nssv577219;nssv577222;nssv577223;nssv577224;nssv577227;nssv577229;nssv577230;nssv577232;nssv577233;nssv577234;nssv577235;nssv577236;nssv577238;nssv577239;nssv577240;nssv577241;nssv577242;nssv577243;nssv577244;nssv578501;nssv578502;nssv578504;nssv578506;nssv578507;nssv578508;nssv578509;nssv578512;nssv578515;nssv578517;nssv578518;nssv578519;nssv578520;nssv578523;nssv578524;nssv578527;nssv578528;nssv578529;nssv578530;nssv578532;nssv578535;nssv578537;nssv578538;nssv578539;nssv578542;nssv579591;nssv579592;nssv579593;nssv579594;nssv579595;nssv579596;nssv579597;nssv579599;nssv579600;nssv579601;nssv579602;nssv579603;nssv579604;nssv579605;nssv579606;nssv579607;nssv579608;nssv579611;nssv579614;nssv579615;nssv579622;nssv579623;nssv579624;nssv579625;nssv579626;nssv579627;nssv579628;nssv579629;nssv579630;nssv579632;nssv579633;nssv579634;nssv579635;nssv579636;nssv579637;nssv579638;nssv579639;nssv579640;nssv579641;nssv579643;nssv579644;nssv579645;nssv579646;nssv579647;nssv579648;nssv579649;nssv579650;nssv579651;nssv579652;nssv579654;nssv579655;nssv579658;nssv579659;nssv579660;nssv579661;nssv579662;nssv579663;nssv579665;nssv579666;nssv580303;nssv581530;nssv581879;nssv582122;nssv582207;nssv582220;nssv582254;nssv582279;nssv582295;nssv582298;nssv582301;nssv582348;nssv582353;nssv582441;nssv582467;nssv582499;nssv582538;nssv582540;nssv582558;nssv582607;nssv582650;nssv582722;nssv582730;nssv582753;nssv582807;nssv582820;nssv582831;nssv582837;nssv582838;nssv582846;nssv582847;nssv582970;nssv583014;nssv583058;nssv583072;nssv583139;nssv583147;nssv583149;nssv583196;nssv583224;nssv583237;nssv583260;nssv583263;nssv583282;nssv583303;nssv583802;nssv583874;nssv583875;nssv583880;nssv584350;nssv584351;nssv584352;nssv584353;nssv584355;nssv584356;nssv584367;nssv584498;nssv584556;nssv585195;nssv585226;nssv585229;nssv585240;nssv585249;nssv585250;nssv677782;nssv699299;nssv706138;nssv706230;nssv706236;nssv706257;nssv706295;nssv706308;nssv706344;nssv706347;nssv706371;nssv706398;nssv706411;nssv706418;nssv706442;nssv706463;nssv706493;nssv706592;nssv706859;nssv707151;nssv707163;nssv723083;nssv7462846;nssv7463028;nssv7463611;nssv7465403;nssv7466249;nssv7466484;nssv7466866;nssv7467289;nssv7472674;nssv7487147;nssv7487148;nssv7487153;nssv7487187;nssv7487211;nssv7487214;nssv7602184;nssv8635342;nssv8639432;nssv8639458;nssv8639516;nssv8639609;nssv8639633;nssv8639810;nssv8639944;nssv8639974;nssv8639988;nssv8639992;nssv8639999	Conflicting interpretations of pathogenicity;Likely pathogenic;Pathogenic;Pathogenic/Likely pathogenic;Uncertain significance;not provided;risk factor	1:100454445-100894444;1:100454445-100934444;1:100454445-101454444;1:100494445-100934444;1:100494445-100974444;1:100494445-101054444;1:100574445-100854444;1:100814445-101454444;1:100854445-101454444;1:100894445-101414444;1:100894445-101454444;1:100894445-101494444;1:100934445-101454444;1:100934445-101494444;1:101014445-101454444;1:101374445-102334444;1:101374445-103054444;1:101414445-102254444;1:101414445-102294444;1:101414445-102374444;1:101414445-102454444	ENCFF039LVJ:ENCFF067UVH:ENCFF139JCA:ENCFF156SZO:ENCFF176FDF:ENCFF183RCR:ENCFF241RXN:ENCFF296RLZ:ENCFF302WDA:ENCFF311BGF:ENCFF444WRK:ENCFF458AHX:ENCFF461GOG:ENCFF572FKA:ENCFF603GAT:ENCFF654ZID:ENCFF716CFF:ENCFF718ETU:ENCFF796ORT:ENCFF822VBC:ENCFF869GJT	0.395	0.400			1:224011690-224016553	(AATGG)n		2.04256583648987	1.79890184043068	1.99663685291374	4.49615398253733	7.85646230843938		3										yes	yes	601691;170995;164690;607008;613665;610113;146920;605205;610624;610860;103320;615790;103020;606811;612866;604566;171760;606014;102770;102771;604774;607245;104770;107670;607560;603024;607999;605481;612316;605537;610513;182310;182340;182330;615291;603517;602144;606412;120550;120570;120575;120950;120960;601013;114208;611501;601896;114250;114251;610162;605554;186780;120920;120920;125240;603504;116952;607393;609443;600236;616690;134370;134371;605336;608593;601525;600031;118507;602024;602023;610036;611140;190197;615623;120280;120252;120260;601924;600650;120620;120650;604210;138971;607657;123860;601405;601105;603448;614566;610956;248610;615820;602202;191311;615464;606418;608172;608375;615730;605951;612779;613360;612666;601365;600423;602201;617987;606273;611813;616846;172430;130500;176946;600997;138295;609017;606351;134580;612309;602935;611026;134638;146760;146790;604590;612169;146740;610665;604973;134629;608897;610595;135940;616284;609144;136132;611539;601094;612280;137163;606953;614998;606463;601176;618128;600871;121013;600897;603324;605425;601749;138290;139370;139340;139380;607983;607468;609245;608317;138090;605998;615684;608374;608548;613898;600234;142622;600713;613890;142461;612801;603491;124092;607562;147880;618051;607199;147571;176262;605411;603305;602208;602983;603537;610044;616758;609132;605393;611279;605995;603286;150310;150292;610389;153390;605747;601007;602146;150330;152445;608869;602600;608271;604094;605102;608205;608507;614397;609831;159530;159440;609023;611978;617619;607093;601231;158340;604933;601652;612176;608862;608515;605254;602985;609607;609607;604043;613121;609145;600727;162030;608700;600275;618025;607215;604766;604766;108780;604630;164790;191315;601902;610339;606755;605347;610363;602533;602533;612036;167410;176310;607786;609023;603427;602859;603867;601791;600279;171900;606879;601730;610273;610274;602839;608309;609712;601975;172411;600522;601192;611101;153454;607622;614787;606822;609853;600923;613257;600722;179755;605557;176763;604283;607301;167420;617413;602177;603673;603155;600716;151460;179590;607204;609275;603615;606077;605313;180040;179820;605226;601863;601499;603276;111700;111680;609591;180435;618016;602336;602943;180069;604175;603634;603702;609595;607529;609321;184755;186357;185470;602413;604188;606210;607292;107300;605593;164780;600682;603941;608744;138140;611146;609617;605632;610804;605763;610299;601019;107310;607223;615242;608241;128260;602458;606077;182860;606494;181590;617853;610949;600104;615463;137290;600774;187040;605078;612805;604127;604614;190370;190220;603031;614123;616101;600315;603594;613932;191045;613931;614512;191030;617840;608756;188540;602617;610538;611632;610554;191540;613521;191523;608400;610132;600533;608877;610035;604733;601968;603490;605237;603623;607860;606480;614159;610568	5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	A3GALT2	NM_001080438	1028	14334	txStart-txEnd	5'UTR-3'UTR	33306765	33321098		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:32435084-34634925_INV														-2.62354415217069	0.668347390481294	-2.47162789907313	2.27028092535663	1.75809197357458	3.6237402371872e-07			61.43											2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	AADACL3	NM_001103170	1228	12652	txStart-txEnd	5'UTR-3'UTR	12716109	12728760		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_568	21462	1	0	4.70000013592653e-05	0.000450999999884516			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV														-0.0099947629380129	-2.53125239294469	-2.47162789907313	0.0361612141503088	-0.109500896056784	0.000110836921442839			92.94											2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	AADACL4	NM_001013630	1228	22541	txStart-txEnd	5'UTR-3'UTR	12644546	12667086		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV														1.11523579451166	-2.53125239294469	-2.47162789907313	0.627786154935008	-1.71767968413379	0.000377692943043426			96.7											2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABCA4	NM_000350	6872	128316	txStart-txEnd	5'UTR-3'UTR	93992833	94121148		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_29		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:93904934-94557082_INV		deletion;duplication	nssv15122535;nssv15755228;nssv15755229;nssv15755230;nssv15755231;nssv15755274	Likely pathogenic;Pathogenic										-0.223265275448233	0.162433062701834	0.0828007325273117	-0.973482043721339	-1.54317890436067	1.53177458885137e-26			18.63						Retinal dystrophy, early-onset severe, 248200 (3)/ Stargardt disease 1, 248200 (3)/ Fundus flavimaculatus, 248200 (3)/ (Macular degeneration, age-related, 2), 153800 (3)/ Cone-rod dystrophy 3, 604116 (3)/ Retinitis pigmentosa 19, 601718 (3)	AR/AR/AR/AD//AR	yes	yes	601691	5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABCD3	NM_002858	2003	100276	txStart-txEnd	5'UTR-3'UTR	94418388	94518663		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_1802	20400	0	1	9.7999996796716e-05	0.000269000011030585	gnomAD_v2_INV_1_29		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:93904934-94557082_INV		deletion	nssv15123654;nssv7487187	Pathogenic										-0.791493397087143	0.758372470037623	0.144850798883807	-0.0657255620211599	2.47749915885857	0.999744635020598			15.03						?Bile acid synthesis defect, congenital, 5, 616278 (3)	AR		yes	170995	3
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABL2	NM_007314	3561	130348	txStart-txEnd	5'UTR-3'UTR	179099330	179229677		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_40		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV	ABL2													0.312084882500471	1.09697789156955	0.971116167575072	-1.08772838090628	1.88712386921967	0.0685656805242374			24.57						Leukemia, acute myeloid, with eosinophilia (1)				164690	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACADM	NM_001286043	1378	39333	txStart-txEnd	5'UTR-3'UTR	75724346	75763678		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_7		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV	DLSTP1	deletion;duplication	nssv15161463;nssv15161709	Likely pathogenic;Pathogenic										0.556328863957891	0.289830550548995	0.472142435542425	0.038662437371825	0.274914641055327	5.34293728836624e-06	30	0	29.48	confirmed	biallelic	loss of function	MEDIUM CHAIN ACYL-COENZYME A DEHYDROGENASE DEFICIENCY	7603790;1684086;7929823;1972503;6434827;11409868;9158144;11349232	Acyl-CoA dehydrogenase, medium chain, deficiency of, 201450 (3)	AR	yes		607008	5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACAP3	NM_030649	2529	15541	txStart-txEnd	5'UTR-3'UTR	1292390	1307930	gssvG1	3	57	0.05263158	gssvL101	26	19585	0.00132755	gnomAD_v2_DUP_1_110	466	2	0	0.004292000085115433	0.0227269995957613			-1	-1	1:1268333-1339037_DUP	3.419e-05	1:83945-209460925_INV	MIR6726/SNORD167													-0.698751770388161	-1.12940910767123	-1.0571002375334	-0.996688596284666	1.93663655704885	0.0854370419522802			73.34											1
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACBD6	NM_032360	857	214349	txStart-txEnd	5'UTR-3'UTR	180288229	180502577		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_2784	20400	1	0	4.8999998398358e-05	0.000134000001708046	gnomAD_v2_INV_1_40		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:107555342-232824950_INV	MIR3121													-0.159927915449793	0.074176193145211	0.018265252602563	-0.0712672100424217	-0.300012422402704	0.0462595976353735			22.84	possible	biallelic	loss of function	AUTOSOMAL RECESSIVE MENTAL RETARDATION	21937992						2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACKR1	NM_001122951	1018	1627	txStart-txEnd	5'UTR-3'UTR	159204874	159206500		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_40		-1	-1	1:159156568-160055297_DUP	3.419e-05	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV																						81.18						(Malaria, vivax, protection against), 611162 (3)/ [Blood group, Duffy system], 110700 (3)/ [White blood cell count QTL], 611862 (3)	/AR, AD/AR		yes	613665	3
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACOT11	NM_015547	1841	90966	txStart-txEnd	5'UTR-3'UTR	54548227	54639192		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_1332;gnomAD_v2_DUP_1_1336	20400;20400	2;1	0;0	9.7999996796716e-05	0.00268799997866154	gnomAD_v2_INV_1_7		-1	-1	1:54380868-54854503_DUP	0.0002393	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:36241391-73134343_INV	FAM151A													-2.62354415217069	-2.53125239294469	-2.47162789907313	0.628589969010047	0.353525599561739	2.10377229994243e-11			54.52											2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACOT7	NM_181864	1152	121498	txStart-txEnd	5'UTR-3'UTR	6264271	6385768		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV	ACOT7													-2.62354415217069	0.56492762227724	-1.88301084526372	0.0670724558623954	2.75661204837795	0.29179891021488			36.89											2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACP6	NM_016361	1297	28296	txStart-txEnd	5'UTR-3'UTR	147642229	147670524	gssvG1762,gssvG1774,gssvG1820	2538	14967	0.16957306	gssvL5089	3	12407	0.00024180	gnomAD_v2_DUP_1_2278	21476	8	0	0.00037299998803064227	0.000658000004477799	gnomAD_v2_DEL_1_9113		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV;1:109177596-154287541_INV;1:120535004-148975895_INV;1:146050179-148404678_INV;1:146229017-149390597_INV;1:146335643-149592694_INV														-2.62354415217069	-2.20556738605708	-2.47162789907313	0.639314452356601	0.455299252801581	0.000620272905557814			61.72											1
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACTG1P20	NR_033926	1	2653	txStart-txEnd	UTR	27323873	27326525		0	0	-1		0	0	-1					-1	-1			-1	-1	1:27190616-27432275_DUP	3.419e-05	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV																																	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACTG1P4	NR_024438	1	1984	txStart-txEnd	UTR	103569403	103571386	gssvG1320,gssvG1324,gssvG1336,gssvG1335,gssvG1342,gssvG1362,gssvG1328,gssvG1363	1298	24985	0.05195117		0	0	-1	gnomAD_v2_DUP_1_1919;gnomAD_v2_DUP_1_1920;gnomAD_v2_DUP_1_1921	19120;20430;21256	41;507;1282	4;266;379	0.09597299993038177	0.139740005135536	gnomAD_v2_INV_1_29	<CN2>;<CN3>	0.0429313	0.0736	1:103366138-105581580_DUP	6.839e-05	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV																																	1

Upper part of second file:

AnnotSV ID	SV chrom	SV start	SV end	SV length	SV type	ID	REF	ALT	QUAL	FILTER	INFO	AnnotSV type	Gene name	NM	CDS length	tx length	location	location2	intersectStart	intersectEnd	DGV_GAIN_IDs	DGV_GAIN_n_samples_with_SV	DGV_GAIN_n_samples_tested	DGV_GAIN_Frequency	DGV_LOSS_IDs	DGV_LOSS_n_samples_with_SV	DGV_LOSS_n_samples_tested	DGV_LOSS_Frequency	GD_ID	GD_AN	GD_N_HET	GD_N_HOMALT	GD_AF	GD_POPMAX_AF	GD_ID_others	1000g_event	1000g_AF	1000g_max_AF	IMH_ID	IMH_AF	IMH_ID_others	promoters	dbVar_event	dbVar_variant	dbVar_status	TADcoordinates	ENCODEexperiments	GCcontent_left	GCcontent_right	Repeats_coord_left	Repeats_type_left	Repeats_coord_right	Repeats_type_right	ACMG	delZ_ExAC	dupZ_ExAC	cnvZ_ExAC	synZ_ExAC	misZ_ExAC	pLI_ExAC	Mim Number	Phenotypes	Inheritance	morbidGenesCandidates	morbidGenes	HI_CGscore	TriS_CGscore	DDD_status	DDD_mode	DDD_consequence	DDD_disease	DDD_pmids	HI_DDDpercent	AnnotSV ranking
1_633720_633721_BND_1	1	633720	633721		BND	MantaBND:3:0:1:0:0:0:1	T	T]chr8:62102872]	.	.	SVTYPE=BND;MATEID=MantaBND:3:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=TC;BND_PAIR_COUNT=6;PAIR_COUNT=6	full									gssvG11,gssvG4,gssvG38,gssvG84	34	19719	0.00172423	gssvL13,gssvL7,gssvL32,gssvL38	22	8400	0.00261905					-1	-1	gnomAD_v2_DUP_1_23;gnomAD_v2_DEL_1_27		-1	-1		-1	1:83945-209460925_INV							0.420	0.420																									2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	full	A3GALT2/AADACL3/AADACL4/ABCA4/ABCD3/ABL2/ACADM/ACAP3/ACBD6/ACKR1/ACOT11/ACOT7/ACP6/ACTG1P20/ACTG1P4/ACTL8/ACTRT2/ADAM15/ADAM30/ADAMTS4/ADAMTSL4/ADAMTSL4-AS1/ADAR/ADCY10/ADGRB2/ADGRL2/ADGRL4/ADIPOR1/ADORA1/ADORA3/ADPRHL2/AGBL4/AGBL4-AS1/AGBL4-IT1/AGL/AGMAT/AGO1/AGO3/AGO4/AGRN/AGTRAP/AHCYL1/AHDC1/AIDA/AIM2/AJAP1/AK2/AK4/AK5/AKIRIN1/AKNAD1/AKR1A1/AKR7A2/AKR7A2P1/AKR7A3/AKR7L/ALDH4A1/ALDH9A1/ALG14/ALG14-AS1/ALG6/ALPL/ALX3/AMIGO1/AMPD1/AMPD2/AMY1A/AMY1B/AMY1C/AMY2A/AMY2B/ANGEL2/ANGPTL1/ANGPTL3/ANGPTL7/ANKRD13C/ANKRD34A/ANKRD35/ANKRD36BP1/ANKRD45/ANKRD65/ANP32E/ANXA9/AP4B1/AP4B1-AS1/APCS/APH1A/APOA2/APOBEC4/AQP10/ARHGAP29/ARHGAP30/ARHGEF10L/ARHGEF11/ARHGEF16/ARHGEF19/ARHGEF2/ARID1A/ARL8A/ARMH1/ARNT/ARPC5/ARTN/ASAP3/ASB17/ASCL5/ASH1L/ASH1L-AS1/ASPM/ASTN1/ATAD3A/ATAD3B/ATAD3C/ATF3/ATF6/ATG4C/ATP13A2/ATP1A1/ATP1A1-AS1/ATP1A2/ATP1A4/ATP1B1/ATP2B4/ATP5IF1/ATP5PB/ATP6V0B/ATP6V1G3/ATP8B2/ATPAF1/ATXN7L2/AUNIP/AURKAIP1/AURKAP1/AVPR1B/AXDND1/AZIN2/B3GALT2/B3GALT6/B4GALT2/B4GALT3/BARHL2/BATF3/BCAN/BCAR3/BCAR3-AS1/BCAS2/BCL10/BCL2L15/BCL9/BEND5/BEST4/BGLAP/BLACAT1/BLZF1/BMP8A/BMP8B/BNIPL/BOLA1/BPNT1/BRDT/BRINP2/BRINP3/BROX/BSDC1/BSND/BTBD19/BTBD8/BTF3L4/BTG2/C1QA/C1QB/C1QC/C1QTNF12/C1orf105/C1orf109/C1orf112/C1orf115/C1orf116/C1orf122/C1orf127/C1orf137/C1orf140/C1orf141/C1orf143/C1orf146/C1orf158/C1orf159/C1orf162/C1orf167/C1orf167-AS1/C1orf174/C1orf185/C1orf189/C1orf194/C1orf195/C1orf21/C1orf210/C1orf216/C1orf220/C1orf226/C1orf232/C1orf43/C1orf50/C1orf52/C1orf53/C1orf54/C1orf56/C1orf61/C1orf68/C1orf74/C1orf87/C1orf94/C2CD4D/C2CD4D-AS1/C4BPA/C4BPB/C8A/C8B/CA14/CA6/CACHD1/CACNA1E/CACNA1S/CACYBP/CADM3/CADM3-AS1/CALML6/CALR4P/CAMK1G/CAMK2N1/CAMSAP2/CAMTA1/CAMTA1-AS2/CAMTA1-DT/CAP1/CAPN2/CAPN8/CAPZA1/CAPZB/CASP9/CASQ1/CASQ2/CASZ1/CATSPER4/CC2D1B/CCDC163/CCDC17/CCDC18/CCDC18-AS1/CCDC181/CCDC185/CCDC190/CCDC24/CCDC27/CCDC28B/CCDC30/CCN1/CCNL2/CCT3/CD101/CD160/CD164L2/CD1A/CD1B/CD1C/CD1D/CD1E/CD2/CD244/CD247/CD34/CD46/CD48/CD52/CD53/CD55/CD58/CD5L/CD84/CDA/CDC14A/CDC20/CDC42/CDC42SE1/CDC7/CDC73/CDCA8/CDCP2/CDK11A/CDK11B/CDK18/CDKN2C/CELA2A/CELA2B/CELA3A/CELA3B/CELF3/CELSR2/CENPF/CENPL/CENPS/CENPS-CORT/CEP104/CEP350/CEP85/CEPT1/CERS2/CFAP126/CFAP45/CFAP57/CFAP74/CFH/CFHR1/CFHR2/CFHR3/CFHR4/CFHR5/CGN/CHD1L/CHD5/CHI3L1/CHI3L2/CHIA/CHIAP2/CHIT1/CHRNB2/CHTOP/CIART/CITED4/CKS1B/CLCA1/CLCA2/CLCA3P/CLCA4/CLCA4-AS1/CLCC1/CLCN6/CLCNKA/CLCNKB/CLDN19/CLIC4/CLK2/CLSPN/CLSTN1/CMPK1/CNKSR1/CNN3/CNR2/CNTN2/COA7/COL11A1/COL16A1/COL24A1/COL8A2/COL9A2/COLGALT2/COP1/COPA/CORT/CPLANE2/CPT2/CPTP/CR1/CR1L/CR2/CRABP2/CRB1/CRCT1/CREB3L4/CREG1/CRNN/CROCC/CROCCP2/CROCCP3/CRP/CRTC2/CRYBG2/CRYZ/CRYZL2P/CRYZL2P-SEC16B/CSDE1/CSF1/CSF3R/CSMD2/CSMD2-AS1/CSRP1/CTBS/CTH/CTNNBIP1/CTPS1/CTRC/CTSE/CTSK/CTSS/CTTNBP2NL/CTXND2/CYB561D1/CYB5R1/CYB5RL/CYCSP52/CYMP/CYMP-AS1/CYP2J2/CYP4A11/CYP4A22/CYP4B1/CYP4X1/CYP4Z1/CYP4Z2P/CZIB/DAB1/DAB1-AS1/DAP3/DARS2/DBT/DCAF6/DCAF8/DCDC2B/DCLRE1B/DCST1/DCST1-AS1/DCST2/DDAH1/DDI2/DDOST/DDR2/DDX20/DDX59/DDX59-AS1/DEDD/DENND1B/DENND2C/DENND2D/DENND4B/DEPDC1/DEPDC1-AS1/DFFA/DFFB/DHCR24/DHDDS/DHDDS-AS1/DHRS3/DHX9/DIO1/DIPK1A/DIRAS3/DISP1/DISP3/DLEU2L/DLGAP3/DLSTP1/DMAP1/DMBX1/DMRTA2/DMRTB1/DNAJA1P5/DNAJB4/DNAJC11/DNAJC16/DNAJC6/DNAJC8/DNALI1/DNASE2B/DNM3/DNM3-IT1/DNM3OS/DNTTIP2/DOCK7/DPH2/DPH5/DPM3/DPT/DPYD/DPYD-AS1/DPYD-AS2/DR1/DRAM2/DRAXIN/DRD5P2/DSTYK/DTL/DUSP10/DUSP12/DUSP23/DUSP27/DVL1/DYRK3/E2F2/EBNA1BP2/ECE1/ECE1-AS1/ECHDC2/ECM1/EDEM3/EDN2/EEF1AKNMT/EFCAB14/EFCAB14-AS1/EFCAB7/EFHD2/EFNA1/EFNA3/EFNA4/EIF2B3/EIF2D/EIF3I/EIF4G3/ELAVL4/ELF3/ELF3-AS1/ELK4/ELOA/ELOA-AS1/ELOVL1/EMBP1/EMC1/EMC1-AS1/ENO1/ENO1-AS1/ENSA/EPB41/EPHA10/EPHA2/EPHA8/EPHB2/EPHX4/EPRS1/EPS15/EPS8L3/ERI3/ERI3-IT1/ERICH3/ERICH3-AS1/ERLNC1/ERMAP/ERRFI1/ESPN/ESPNP/ESRRG/ETNK2/ETV3/ETV3L/EVA1B/EVI5/EXO5/EXOSC10/EXOSC10-AS1/EXTL1/EXTL2/EYA3/F11R/F13B/F3/F5/FAAH/FAAHP1/FAAP20/FABP3/FAF1/FALEC/FAM102B/FAM110D/FAM131C/FAM151A/FAM163A/FAM167B/FAM177B/FAM183A/FAM189B/FAM20B/FAM229A/FAM41C/FAM43B/FAM71A/FAM72A/FAM72B/FAM72C/FAM72D/FAM76A/FAM78B/FAM87B/FASLG/FBLIM1/FBXO2/FBXO42/FBXO44/FBXO6/FCAMR/FCER1A/FCER1G/FCGR1A/FCGR1B/FCGR1CP/FCGR2A/FCGR2B/FCGR2C/FCGR3A/FCGR3B/FCMR/FCN3/FCRL1/FCRL2/FCRL3/FCRL4/FCRL5/FCRL6/FCRLA/FCRLB/FDPS/FGGY/FGR/FHAD1/FHAD1-AS1/FHL3/FLAD1/FLG/FLG-AS1/FLG2/FLJ37453/FLVCR1/FLVCR1-DT/FMO1/FMO2/FMO3/FMO4/FMO5/FMO6P/FMO9P/FMOD/FNBP1L/FNDC10/FNDC5/FNDC7/FOXD2/FOXD2-AS1/FOXD3/FOXD3-AS1/FOXE3/FOXJ3/FOXO6/FOXO6-AS1/FPGT/FPGT-TNNI3K/FRRS1/FUBP1/FUCA1/FYB2/G0S2/GABPB2/GABRD/GADD45A/GALE/GAS5/GAS5-AS1/GATAD2B/GBA/GBAP1/GBAT2/GBP1/GBP1P1/GBP2/GBP3/GBP4/GBP5/GBP6/GBP7/GCLM/GDAP2/GEMIN8P4/GFI1/GIPC2/GJA4/GJA5/GJA8/GJA9/GJA9-MYCBP/GJB3/GJB4/GJB5/GLIS1/GLMN/GLMP/GLRX2/GLUL/GMEB1/GNAI3/GNAT2/GNB1/GNG12/GNG12-AS1/GNG5/GNL2/GNRHR2/GOLPH3L/GOLT1A/GON4L/GORAB/GORAB-AS1/GPA33/GPATCH2/GPATCH3/GPATCH4/GPBP1L1/GPN2/GPR153/GPR157/GPR161/GPR25/GPR3/GPR37L1/GPR52/GPR61/GPR88/GPR89A/GPR89B/GPSM2/GPX7/GRHL3/GRIK3/GS1-279B7.1/GSTM1/GSTM2/GSTM3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11/SRSF4/SSBP3/SSBP3-AS1/SSR2/SSU72/SSX2IP/ST3GAL3/ST6GALNAC3/ST6GALNAC5/ST7L/STIL/STK40/STMN1/STPG1/STRIP1/STX12/STX6/STXBP3/SUCO/SUMO1P3/SUSD4/SV2A/SVBP/SWT1/SYCP1/SYDE2/SYF2/SYNC/SYPL2/SYT11/SYT14/SYT2/SYT6/SYTL1/SZRD1/SZT2/SZT2-AS1/TACSTD2/TADA1/TAF12/TAF13/TAF1A/TAF1A-AS1/TAFA3/TAGLN2/TAL1/TARDBP/TARS2/TAS1R1/TAS1R2/TAS1R3/TATDN3/TBX15/TBX19/TCEA3/TCEANC2/TCHH/TCHHL1/TCTEX1D1/TCTEX1D4/TDRD10/TDRD5/TDRKH/TDRKH-AS1/TEDDM1/TEKT2/TENT5B/TENT5C/TESK2/TEX35/TEX38/TEX46/TEX50/TFAP2E/TGFB2/TGFB2-AS1/TGFB2-OT1/TGFBR3/THAP3/THBS3/THEM4/THEM5/THEMIS2/THRAP3/TIE1/TIMM17A/TINAGL1/TIPRL/TLCD4/TLCD4-RWDD3/TLR5/TM2D1/TMCC2/TMCO1/TMCO1-AS1/TMCO2/TMCO4/TMED5/TMEM125/TMEM167B/TMEM183A/TMEM200B/TMEM201/TMEM222/TMEM234/TMEM240/TMEM269/TMEM269-DT/TMEM274P/TMEM275/TMEM35B/TMEM39B/TMEM50A/TMEM51/TMEM51-AS1/TMEM52/TMEM53/TMEM54/TMEM59/TMEM61/TMEM69/TMEM79/TMEM81/TMEM82/TMEM88B/TMEM9/TMIGD3/TMOD4/TNFAIP8L2/TNFAIP8L2-SCNM1/TNFRSF14/TNFRSF14-AS1/TNFRSF18/TNFRSF1B/TNFRSF25/TNFRSF4/TNFRSF8/TNFRSF9/TNFSF18/TNFSF4/TNN/TNNI1/TNNI3K/TNNT2/TNR/TOE1/TOMM40L/TOP1P1/TOR1AIP1/TOR1AIP2/TOR3A/TP53BP2/TP73/TP73-AS1/TPM3/TPR/TPRG1L/TRABD2B/TRAF3IP3/TRAF5/TRAPPC3/TRIM33/TRIM45/TRIM46/TRIM62/TRIM63/TRIT1/TRMT13/TRMT1L/TRNAU1AP/TRNP1/TSACC/TSEN15/TSHB/TSPAN1/TSPAN2/TSSK3/TSTD1/TTC22/TTC24/TTC34/TTC39A/TTC39A-AS1/TTC4/TTF2/TTLL10/TTLL7/TUFT1/TUT4/TXLNA/TXNDC12/TXNDC12-AS1/TXNIP/TYW3/UAP1/UBAP2L/UBE2J2/UBE2Q1/UBE2Q1-AS1/UBE2T/UBE2U/UBE4B/UBIAD1/UBL4B/UBQLN4/UBR4/UBXN10/UBXN10-AS1/UBXN11/UCHL5/UCK2/UFC1/UHMK1/UOX/UQCRH/UQCRHL/UROD/USF1/USH2A/USP1/USP21/USP24/USP33/USP48/UTP11/UTP25/UTS2/VAMP3/VAMP4/VANGL1/VANGL2/VASH2/VAV3/VAV3-AS1/VCAM1/VHLL/VPS13D/VPS45/VPS72/VSIG8/VTCN1/VWA1/VWA5B1/WARS2/WARS2-AS1/WARS2-IT1/WASF2/WDR3/WDR47/WDR63/WDR77/WDR78/WDTC1/WLS/WNT2B/WNT4/WRAP73/XCL1/XCL2/XKR8/XPR1/YARS1/YBX1/YIPF1/YOD1/YRDC/YTHDF2/YY1AP1/ZBED6/ZBTB17/ZBTB37/ZBTB40/ZBTB41/ZBTB48/ZBTB7B/ZBTB8A/ZBTB8B/ZBTB8OS/ZC3H11A/ZC3H11B/ZC3H12A/ZCCHC17/ZDHHC18/ZFP69/ZFP69B/ZFYVE9/ZMPSTE24/ZMYM1/ZMYM4/ZMYM4-AS1/ZMYM6/ZMYND12/ZNF281/ZNF326/ZNF362/ZNF436/ZNF436-AS1/ZNF593/ZNF644/ZNF648/ZNF683/ZNF684/ZNF687/ZNF687-AS1/ZNF691/ZNF697/ZNHIT6/ZPLD2P/ZRANB2/ZRANB2-AS1/ZRANB2-AS2/ZSCAN20/ZSWIM5/ZYG11A/ZYG11B/ZZZ3	copy_number_gain;copy_number_loss;deletion;duplication	essv4368444;nssv1157165;nssv1157168;nssv1157189;nssv1157193;nssv1157214;nssv1157217;nssv1157250;nssv1157273;nssv1157274;nssv1157306;nssv1157307;nssv1157308;nssv1157309;nssv1157311;nssv1157315;nssv1157875;nssv13638693;nssv13638713;nssv13638840;nssv13638876;nssv13638979;nssv13638987;nssv13639292;nssv13639373;nssv13639487;nssv13639504;nssv13639620;nssv13639665;nssv13639713;nssv13640035;nssv13640262;nssv13640286;nssv13640404;nssv13640535;nssv13640569;nssv13640623;nssv13640672;nssv13640809;nssv13641138;nssv13641147;nssv13641189;nssv13641209;nssv13641247;nssv13641271;nssv13641324;nssv13641350;nssv13642021;nssv13642151;nssv13642154;nssv13642383;nssv13642390;nssv13642590;nssv13642778;nssv13643109;nssv13643277;nssv13643278;nssv13643714;nssv13643716;nssv13644070;nssv13644157;nssv13644718;nssv13644720;nssv13644784;nssv13644918;nssv13645225;nssv13645443;nssv13645530;nssv13646223;nssv13646455;nssv13646717;nssv13647205;nssv13647265;nssv13647315;nssv13647423;nssv13647497;nssv13647559;nssv13647615;nssv13648427;nssv13648455;nssv13648557;nssv13648612;nssv13648634;nssv13648744;nssv13648889;nssv13648971;nssv13649175;nssv13649365;nssv13649375;nssv13649432;nssv13649466;nssv13649968;nssv13649989;nssv13650373;nssv13650602;nssv13650648;nssv13650929;nssv13651000;nssv13651072;nssv13651277;nssv13651479;nssv13651574;nssv13651583;nssv13651645;nssv13651859;nssv13652057;nssv13652240;nssv13652345;nssv13652463;nssv13652903;nssv13653083;nssv13653093;nssv13653103;nssv13653129;nssv13653198;nssv13653218;nssv13653300;nssv13653365;nssv13653606;nssv13653667;nssv13653687;nssv13654185;nssv13654197;nssv13654255;nssv13654261;nssv13654326;nssv13654496;nssv13654536;nssv13654566;nssv13654929;nssv13654953;nssv13655057;nssv13655179;nssv13655235;nssv13655558;nssv13655807;nssv13656051;nssv13656120;nssv13656441;nssv13656517;nssv13656566;nssv14081994;nssv14081997;nssv14082061;nssv14082144;nssv14082163;nssv14082177;nssv14082244;nssv14082308;nssv14082318;nssv14082321;nssv14082355;nssv14082394;nssv14082395;nssv14082408;nssv14082499;nssv14082523;nssv1415016;nssv1415217;nssv1415280;nssv1415282;nssv1415285;nssv1415305;nssv1415327;nssv1415329;nssv1415401;nssv1415419;nssv1415490;nssv1415513;nssv1415519;nssv1494821;nssv1494822;nssv1494823;nssv1494824;nssv1494826;nssv1494827;nssv1494828;nssv1494829;nssv1494831;nssv1494832;nssv1494833;nssv1494834;nssv1494835;nssv1494836;nssv1494837;nssv1494838;nssv1494840;nssv1494841;nssv1494842;nssv1494843;nssv1494844;nssv1495166;nssv1495167;nssv1495168;nssv1495722;nssv15119723;nssv15119728;nssv15119731;nssv15119768;nssv15119931;nssv15119937;nssv15119938;nssv15119939;nssv15119944;nssv15120115;nssv15120130;nssv15120157;nssv15120191;nssv15120196;nssv15120201;nssv15120497;nssv15120751;nssv15120755;nssv15120756;nssv15121047;nssv15121050;nssv15121100;n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15770172;nssv15770192;nssv15770194;nssv15770215;nssv15770230;nssv15770284;nssv15770286;nssv15770324;nssv15770412;nssv15770418;nssv15770420;nssv15770429;nssv15770457;nssv15770522;nssv15770527;nssv15770533;nssv15770545;nssv15770606;nssv15770626;nssv15770645;nssv15770728;nssv15770744;nssv15770764;nssv15770765;nssv15770795;nssv15770850;nssv15770858;nssv15770860;nssv15770901;nssv15770973;nssv15770994;nssv15771000;nssv15771042;nssv15771044;nssv15771413;nssv15771414;nssv15771415;nssv15771416;nssv15771417;nssv15771418;nssv15771419;nssv15771460;nssv15771461;nssv15771469;nssv15771480;nssv15771484;nssv15771494;nssv15771498;nssv15771528;nssv15771586;nssv15771607;nssv15771652;nssv15771746;nssv15771750;nssv15771763;nssv15771771;nssv15771790;nssv15771818;nssv15772052;nssv15772355;nssv15772838;nssv15773206;nssv15773642;nssv15773680;nssv15773714;nssv15773719;nssv15773720;nssv15773733;nssv15773734;nssv15773735;nssv15773738;nssv15773765;nssv15773787;nssv15773788;nssv15773792;nssv15773818;nssv15773826;nssv15773849;nssv15773933;nssv15773952;nssv15773956;nssv15773962;nssv15774107;nssv15774128;nssv15774138;nssv15774159;nssv15774161;nssv15774344;nssv15774627;nssv15775494;nssv15775904;nssv15776177;nssv15776374;nssv15776405;nssv15776578;nssv15776768;nssv15776860;nssv15776866;nssv15776867;nssv15776877;nssv15776884;nssv15776888;nssv15776891;nssv15776892;nssv15776900;nssv15776903;nssv15776906;nssv15776916;nssv15776917;nssv15776928;nssv15776937;nssv15776942;nssv15777025;nssv15777031;nssv15777034;nssv15777043;nssv15777243;nssv15777298;nssv15777321;nssv15777369;nssv15777491;nssv15777494;nssv15777505;nssv15777538;nssv15777556;nssv15777589;nssv15777605;nssv15777609;nssv15777638;nssv15777646;nssv15777685;nssv15777715;nssv15777717;nssv15777730;nssv15777747;nssv15777764;nssv1601514;nssv1601722;nssv1601816;nssv1601987;nssv1602013;nssv1602095;nssv1602144;nssv1602148;nssv1602152;nssv1602217;nssv1602221;nssv1602225;nssv1602226;nssv1602228;nssv1602237;nssv1602242;nssv1602489;nssv1602495;nssv1602523;nssv1602734;nssv1602972;nssv1602989;nssv1602993;nssv1603181;nssv1603197;nssv1603536;nssv1603664;nssv1603787;nssv1603793;nssv1603980;nssv1604112;nssv1604129;nssv1604131;nssv1604136;nssv1604142;nssv1604154;nssv1604194;nssv1604364;nssv1604370;nssv1604393;nssv1604655;nssv1604674;nssv1604767;nssv1604929;nssv1607568;nssv1607648;nssv1608111;nssv1608112;nssv1608157;nssv1608159;nssv1608217;nssv1608266;nssv1608295;nssv1608846;nssv1608908;nssv1609140;nssv1609251;nssv1609366;nssv1609367;nssv1609369;nssv1609602;nssv1609603;nssv1610085;nssv1610100;nssv1610103;nssv1610127;nssv1610143;nssv1610261;nssv1610268;nssv1610367;nssv1610374;nssv1610405;nssv1610445;nssv1610446;nssv1610454;nssv1610460;nssv1610617;nssv1610683;nssv1610691;nssv1610695;nssv1610715;nssv1610742;nssv1610746;nssv1610798;nssv1610825;nssv1610911;nssv1610948;nssv1610998;nssv1611053;nssv1611070;nssv1611125;nssv1611163;nssv1611222;nssv1611228;nssv1611343;nssv1611363;nssv1611397;nssv1611471;nssv1611477;nssv1611482;nssv1611558;nssv1611567;nssv1611612;nssv1611625;nssv1611637;nssv1611666;nssv1611701;nssv1611725;nssv1611759;nssv1611802;nssv1611809;nssv1611841;nssv1611845;nssv1611862;nssv1611900;nssv1611901;nssv1611954;nssv1612001;nssv1612030;nssv1612055;nssv1612087;nssv1612097;nssv1612105;nssv1612117;nssv1612189;nssv1612197;nssv1612258;nssv1612290;nssv1612317;nssv1612321;nssv1612364;nssv1612388;nssv1612403;nssv1612433;nssv1612454;nssv1612458;nssv1612497;nssv1612506;nssv1612529;nssv1612536;nssv1612627;nssv1612653;nssv1612699;nssv1612753;nssv1612754;nssv1612815;nssv1612825;nssv1614058;nssv2767595;nssv3394988;nssv3395098;nssv3395100;nssv3395202;nssv3395279;nssv3395311;nssv3395459;nssv3395509;nssv3395745;nssv3395752;nssv3395783;nssv3395996;nssv3396032;nssv3396046;nssv3396064;nssv3396112;nssv3396128;nssv3396288;nssv3396309;nssv3396358;nssv3396378;nssv3396407;nssv3396408;nssv3396444;nssv3396454;nssv3396489;nssv3396509;nssv3396606;nssv3396607;nssv3396638;nssv3396640;nssv3396731;nssv3396744;nssv3396886;nssv3397008;nssv3397095;nssv3397132;nssv3397176;nssv3397270;nssv3397381;nssv3397436;nssv3443291;nssv3445546;nssv3445882;nssv3446048;nssv3447232;nssv3448513;nssv3450228;nssv3450308;nssv3452442;nssv3453616;nssv3454617;nssv3455079;nssv3456133;nssv3457122;nssv3457499;nssv3458389;nssv3459009;nssv3460391;nssv3462607;nssv3487351;nssv3497102;nssv3761542;nssv3761544;nssv3761549;nssv3761593;nssv3761620;nssv451365;nssv575269;nssv575320;nssv575321;nssv575399;nssv575445;nssv575446;nssv575447;nssv575658;nssv575679;nssv575720;nssv575740;nssv575864;nssv575868;nssv575896;nssv575948;nssv576063;nssv576149;nssv576212;nssv576287;nssv576295;nssv576300;nssv576309;nssv576311;nssv576338;nssv576345;nssv576346;nssv576394;nssv576459;nssv576468;nssv576489;nssv576618;nssv576639;nssv576645;nssv576927;nssv576931;nssv576933;nssv576934;nssv576935;nssv576936;nssv576938;nssv576939;nssv576940;nssv576941;nssv576942;nssv576945;nssv576946;nssv576947;nssv576949;nssv576952;nssv576954;nssv576955;nssv577125;nssv577127;nssv577128;nssv577129;nssv577130;nssv577131;nssv577133;nssv577134;nssv577135;nssv577136;nssv577138;nssv577139;nssv577140;nssv577141;nssv577142;nssv577143;nssv577144;nssv577150;nssv577152;nssv577154;nssv577155;nssv577156;nssv577157;nssv577158;nssv577160;nssv577161;nssv577162;nssv577164;nssv577165;nssv577166;nssv577167;nssv577168;nssv577171;nssv577174;nssv577176;nssv577179;nssv577180;nssv577183;nssv577184;nssv577185;nssv577186;nssv577187;nssv577188;nssv577189;nssv577190;nssv577191;nssv577194;nssv577196;nssv577197;nssv577198;nssv577199;nssv577200;nssv577201;nssv577202;nssv577204;nssv577205;nssv577206;nssv577207;nssv577208;nssv577209;nssv577210;nssv577211;nssv577212;nssv577216;nssv577217;nssv577218;nssv577219;nssv577222;nssv577223;nssv577224;nssv577227;nssv577229;nssv577230;nssv577232;nssv577233;nssv577234;nssv577235;nssv577236;nssv577238;nssv577239;nssv577240;nssv577241;nssv577242;nssv577243;nssv577244;nssv578501;nssv578502;nssv578504;nssv578506;nssv578507;nssv578508;nssv578509;nssv578512;nssv578515;nssv578517;nssv578518;nssv578519;nssv578520;nssv578523;nssv578524;nssv578527;nssv578528;nssv578529;nssv578530;nssv578532;nssv578535;nssv578537;nssv578538;nssv578539;nssv578542;nssv579591;nssv579592;nssv579593;nssv579594;nssv579595;nssv579596;nssv579597;nssv579599;nssv579600;nssv579601;nssv579602;nssv579603;nssv579604;nssv579605;nssv579606;nssv579607;nssv579608;nssv579611;nssv579614;nssv579615;nssv579622;nssv579623;nssv579624;nssv579625;nssv579626;nssv579627;nssv579628;nssv579629;nssv579630;nssv579632;nssv579633;nssv579634;nssv579635;nssv579636;nssv579637;nssv579638;nssv579639;nssv579640;nssv579641;nssv579643;nssv579644;nssv579645;nssv579646;nssv579647;nssv579648;nssv579649;nssv579650;nssv579651;nssv579652;nssv579654;nssv579655;nssv579658;nssv579659;nssv579660;nssv579661;nssv579662;nssv579663;nssv579665;nssv579666;nssv580303;nssv581530;nssv581879;nssv582122;nssv582207;nssv582220;nssv582254;nssv582279;nssv582295;nssv582298;nssv582301;nssv582348;nssv582353;nssv582441;nssv582467;nssv582499;nssv582538;nssv582540;nssv582558;nssv582607;nssv582650;nssv582722;nssv582730;nssv582753;nssv582807;nssv582820;nssv582831;nssv582837;nssv582838;nssv582846;nssv582847;nssv582970;nssv583014;nssv583058;nssv583072;nssv583139;nssv583147;nssv583149;nssv583196;nssv583224;nssv583237;nssv583260;nssv583263;nssv583282;nssv583303;nssv583802;nssv583874;nssv583875;nssv583880;nssv584350;nssv584351;nssv584352;nssv584353;nssv584355;nssv584356;nssv584367;nssv584498;nssv584556;nssv585195;nssv585226;nssv585229;nssv585240;nssv585249;nssv585250;nssv677782;nssv699299;nssv706138;nssv706230;nssv706236;nssv706257;nssv706295;nssv706308;nssv706344;nssv706347;nssv706371;nssv706398;nssv706411;nssv706418;nssv706442;nssv706463;nssv706493;nssv706592;nssv706859;nssv707151;nssv707163;nssv723083;nssv7462846;nssv7463028;nssv7463611;nssv7465403;nssv7466249;nssv7466484;nssv7466866;nssv7467289;nssv7472674;nssv7487147;nssv7487148;nssv7487153;nssv7487187;nssv7487211;nssv7487214;nssv7602184;nssv8635342;nssv8639432;nssv8639458;nssv8639516;nssv8639609;nssv8639633;nssv8639810;nssv8639944;nssv8639974;nssv8639988;nssv8639992;nssv8639999	Conflicting interpretations of pathogenicity;Likely pathogenic;Pathogenic;Pathogenic/Likely pathogenic;Uncertain significance;not provided;risk factor	1:100454445-100894444;1:100454445-100934444;1:100454445-101454444;1:100494445-100934444;1:100494445-100974444;1:100494445-101054444;1:100574445-100854444;1:100814445-101454444;1:100854445-101454444;1:100894445-101414444;1:100894445-101454444;1:100894445-101494444;1:100934445-101454444;1:100934445-101494444;1:101014445-101454444;1:101374445-102334444;1:101374445-103054444;1:101414445-102254444;1:101414445-102294444;1:101414445-102374444;1:101414445-102454444	ENCFF039LVJ:ENCFF067UVH:ENCFF139JCA:ENCFF156SZO:ENCFF176FDF:ENCFF183RCR:ENCFF241RXN:ENCFF296RLZ:ENCFF302WDA:ENCFF311BGF:ENCFF444WRK:ENCFF458AHX:ENCFF461GOG:ENCFF572FKA:ENCFF603GAT:ENCFF654ZID:ENCFF716CFF:ENCFF718ETU:ENCFF796ORT:ENCFF822VBC:ENCFF869GJT	0.395	0.400			1:224011690-224016553	(AATGG)n		2.04256583648987	1.79890184043068	1.99663685291374	4.49615398253733	7.85646230843938		601691;170995;164690;607008;613665;610113;146920;605205;610624;610860;103320;615790;103020;606811;612866;604566;171760;606014;102770;102771;604774;607245;104770;107670;607560;603024;607999;605481;612316;605537;610513;182310;182340;182330;615291;603517;602144;606412;120550;120570;120575;120950;120960;601013;114208;611501;601896;114250;114251;610162;605554;186780;120920;120920;125240;603504;116952;607393;609443;600236;616690;134370;134371;605336;608593;601525;600031;118507;602024;602023;610036;611140;190197;615623;120280;120252;120260;601924;600650;120620;120650;604210;138971;607657;123860;601405;601105;603448;614566;610956;248610;615820;602202;191311;615464;606418;608172;608375;615730;605951;612779;613360;612666;601365;600423;602201;617987;606273;611813;616846;172430;130500;176946;600997;138295;609017;606351;134580;612309;602935;611026;134638;146760;146790;604590;612169;146740;610665;604973;134629;608897;610595;135940;616284;609144;136132;611539;601094;612280;137163;606953;614998;606463;601176;618128;600871;121013;600897;603324;605425;601749;138290;139370;139340;139380;607983;607468;609245;608317;138090;605998;615684;608374;608548;613898;600234;142622;600713;613890;142461;612801;603491;124092;607562;147880;618051;607199;147571;176262;605411;603305;602208;602983;603537;610044;616758;609132;605393;611279;605995;603286;150310;150292;610389;153390;605747;601007;602146;150330;152445;608869;602600;608271;604094;605102;608205;608507;614397;609831;159530;159440;609023;611978;617619;607093;601231;158340;604933;601652;612176;608862;608515;605254;602985;609607;609607;604043;613121;609145;600727;162030;608700;600275;618025;607215;604766;604766;108780;604630;164790;191315;601902;610339;606755;605347;610363;602533;602533;612036;167410;176310;607786;609023;603427;602859;603867;601791;600279;171900;606879;601730;610273;610274;602839;608309;609712;601975;172411;600522;601192;611101;153454;607622;614787;606822;609853;600923;613257;600722;179755;605557;176763;604283;607301;167420;617413;602177;603673;603155;600716;151460;179590;607204;609275;603615;606077;605313;180040;179820;605226;601863;601499;603276;111700;111680;609591;180435;618016;602336;602943;180069;604175;603634;603702;609595;607529;609321;184755;186357;185470;602413;604188;606210;607292;107300;605593;164780;600682;603941;608744;138140;611146;609617;605632;610804;605763;610299;601019;107310;607223;615242;608241;128260;602458;606077;182860;606494;181590;617853;610949;600104;615463;137290;600774;187040;605078;612805;604127;604614;190370;190220;603031;614123;616101;600315;603594;613932;191045;613931;614512;191030;617840;608756;188540;602617;610538;611632;610554;191540;613521;191523;608400;610132;600533;608877;610035;604733;601968;603490;605237;603623;607860;606480;614159;610568			yes	yes	3								5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	A3GALT2	NM_001080438	1028	14334	txStart-txEnd	5'UTR-3'UTR	33306765	33321098		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:32435084-34634925_INV														-2.62354415217069	0.668347390481294	-2.47162789907313	2.27028092535663	1.75809197357458	3.6237402371872e-07													61.43	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	AADACL3	NM_001103170	1228	12652	txStart-txEnd	5'UTR-3'UTR	12716109	12728760		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_568	21462	1	0	4.70000013592653e-05	0.000450999999884516			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV														-0.0099947629380129	-2.53125239294469	-2.47162789907313	0.0361612141503088	-0.109500896056784	0.000110836921442839													92.94	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	AADACL4	NM_001013630	1228	22541	txStart-txEnd	5'UTR-3'UTR	12644546	12667086		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV														1.11523579451166	-2.53125239294469	-2.47162789907313	0.627786154935008	-1.71767968413379	0.000377692943043426													96.7	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABCA4	NM_000350	6872	128316	txStart-txEnd	5'UTR-3'UTR	93992833	94121148		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_29		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:93904934-94557082_INV		deletion;duplication	nssv15122535;nssv15755228;nssv15755229;nssv15755230;nssv15755231;nssv15755274	Likely pathogenic;Pathogenic										-0.223265275448233	0.162433062701834	0.0828007325273117	-0.973482043721339	-1.54317890436067	1.53177458885137e-26	601691	Retinal dystrophy, early-onset severe, 248200 (3)/ Stargardt disease 1, 248200 (3)/ Fundus flavimaculatus, 248200 (3)/ (Macular degeneration, age-related, 2), 153800 (3)/ Cone-rod dystrophy 3, 604116 (3)/ Retinitis pigmentosa 19, 601718 (3)	AR/AR/AR/AD//AR	yes	yes								18.63	5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABCD3	NM_002858	2003	100276	txStart-txEnd	5'UTR-3'UTR	94418388	94518663		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_1802	20400	0	1	9.7999996796716e-05	0.000269000011030585	gnomAD_v2_INV_1_29		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:93904934-94557082_INV		deletion	nssv15123654;nssv7487187	Pathogenic										-0.791493397087143	0.758372470037623	0.144850798883807	-0.0657255620211599	2.47749915885857	0.999744635020598	170995	?Bile acid synthesis defect, congenital, 5, 616278 (3)	AR	yes									15.03	4
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ABL2	NM_007314	3561	130348	txStart-txEnd	5'UTR-3'UTR	179099330	179229677		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_40		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV	ABL2													0.312084882500471	1.09697789156955	0.971116167575072	-1.08772838090628	1.88712386921967	0.0685656805242374	164690	Leukemia, acute myeloid, with eosinophilia (1)											24.57	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACADM	NM_001286043	1378	39333	txStart-txEnd	5'UTR-3'UTR	75724346	75763678		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_7		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:68663391-188869781_INV	DLSTP1	deletion;duplication	nssv15161463;nssv15161709	Likely pathogenic;Pathogenic										0.556328863957891	0.289830550548995	0.472142435542425	0.038662437371825	0.274914641055327	5.34293728836624e-06	607008	Acyl-CoA dehydrogenase, medium chain, deficiency of, 201450 (3)	AR		yes	30	0	confirmed	biallelic	loss of function	MEDIUM CHAIN ACYL-COENZYME A DEHYDROGENASE DEFICIENCY	7603790;1684086;7929823;1972503;6434827;11409868;9158144;11349232	29.48	5
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACAP3	NM_030649	2529	15541	txStart-txEnd	5'UTR-3'UTR	1292390	1307930	gssvG1	3	57	0.05263158	gssvL101	26	19585	0.00132755	gnomAD_v2_DUP_1_110	466	2	0	0.004292000085115433	0.0227269995957613			-1	-1	1:1268333-1339037_DUP	3.419e-05	1:83945-209460925_INV	MIR6726/SNORD167													-0.698751770388161	-1.12940910767123	-1.0571002375334	-0.996688596284666	1.93663655704885	0.0854370419522802													73.34	1
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACBD6	NM_032360	857	214349	txStart-txEnd	5'UTR-3'UTR	180288229	180502577		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_2784	20400	1	0	4.8999998398358e-05	0.000134000001708046	gnomAD_v2_INV_1_40		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:107555342-232824950_INV	MIR3121													-0.159927915449793	0.074176193145211	0.018265252602563	-0.0712672100424217	-0.300012422402704	0.0462595976353735								possible	biallelic	loss of function	AUTOSOMAL RECESSIVE MENTAL RETARDATION	21937992	22.84	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACKR1	NM_001122951	1018	1627	txStart-txEnd	5'UTR-3'UTR	159204874	159206500		0	0	-1		0	0	-1					-1	-1	gnomAD_v2_INV_1_40		-1	-1	1:159156568-160055297_DUP	3.419e-05	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV																				613665	(Malaria, vivax, protection against), 611162 (3)/ [Blood group, Duffy system], 110700 (3)/ [White blood cell count QTL], 611862 (3)	/AR, AD/AR	yes									81.18	4
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACOT11	NM_015547	1841	90966	txStart-txEnd	5'UTR-3'UTR	54548227	54639192		0	0	-1		0	0	-1	gnomAD_v2_DUP_1_1332;gnomAD_v2_DUP_1_1336	20400;20400	2;1	0;0	9.7999996796716e-05	0.00268799997866154	gnomAD_v2_INV_1_7		-1	-1	1:54380868-54854503_DUP	0.0002393	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:31594522-94732184_INV;1:36241391-73134343_INV	FAM151A													-2.62354415217069	-2.53125239294469	-2.47162789907313	0.628589969010047	0.353525599561739	2.10377229994243e-11													54.52	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACOT7	NM_181864	1152	121498	txStart-txEnd	5'UTR-3'UTR	6264271	6385768		0	0	-1		0	0	-1					-1	-1			-1	-1		-1	1:83945-209460925_INV	ACOT7													-2.62354415217069	0.56492762227724	-1.88301084526372	0.0670724558623954	2.75661204837795	0.29179891021488													36.89	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACP6	NM_016361	1297	28296	txStart-txEnd	5'UTR-3'UTR	147642229	147670524	gssvG1762,gssvG1774,gssvG1820	2538	14967	0.16957306	gssvL5089	3	12407	0.00024180	gnomAD_v2_DUP_1_2278	21476	8	0	0.00037299998803064227	0.000658000004477799	gnomAD_v2_DEL_1_9113		-1	-1		-1	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV;1:107555342-232824950_INV;1:109177596-154287541_INV;1:120535004-148975895_INV;1:146050179-148404678_INV;1:146229017-149390597_INV;1:146335643-149592694_INV														-2.62354415217069	-2.20556738605708	-2.47162789907313	0.639314452356601	0.455299252801581	0.000620272905557814													61.72	1
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACTG1P20	NR_033926	1	2653	txStart-txEnd	UTR	27323873	27326525		0	0	-1		0	0	-1					-1	-1			-1	-1	1:27190616-27432275_DUP	3.419e-05	1:83945-209460925_INV;1:7601937-50381771_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV																																	2
1_789487_224014522_DUP_1	1	789487	224014522	223225035	DUP	MantaDUP:TANDEM:9:0:2:0:0:0	G	<DUP:TANDEM>	.	.	END=224014522;SVTYPE=DUP;SVLEN=223225035;IMPRECISE;CIPOS=-194,195;CIEND=-254,254;UPSTREAM_PAIR_COUNT=20;DOWNSTREAM_PAIR_COUNT=22;PAIR_COUNT=20	split	ACTG1P4	NR_024438	1	1984	txStart-txEnd	UTR	103569403	103571386	gssvG1320,gssvG1324,gssvG1336,gssvG1335,gssvG1342,gssvG1362,gssvG1328,gssvG1363	1298	24985	0.05195117		0	0	-1	gnomAD_v2_DUP_1_1919;gnomAD_v2_DUP_1_1920;gnomAD_v2_DUP_1_1921	19120;20430;21256	41;507;1282	4;266;379	0.09597299993038177	0.139740005135536	gnomAD_v2_INV_1_29	<CN2>;<CN3>	0.0429313	0.0736	1:103366138-105581580_DUP	6.839e-05	1:83945-209460925_INV;1:9525496-193637393_INV;1:10187872-186857210_INV;1:16798093-234784887_INV;1:24738218-238056495_INV;1:68663391-188869781_INV;1:75962659-179353269_INV																																	1

It can be diffucult to see difference first, but here it is:

AnnotSV ID	SV chrom	SV start	SV end	SV length	SV type	ID	REF	ALT	QUAL	FILTER	INFO	AnnotSV type	Gene name	NM	CDS length	tx length	location	location2	intersectStart	intersectEnd	DGV_GAIN_IDs	DGV_GAIN_n_samples_with_SV	DGV_GAIN_n_samples_tested	DGV_GAIN_Frequency	DGV_LOSS_IDs	DGV_LOSS_n_samples_with_SV	DGV_LOSS_n_samples_tested	DGV_LOSS_Frequency	GD_ID	GD_AN	GD_N_HET	GD_N_HOMALT	GD_AF	GD_POPMAX_AF	GD_ID_others	1000g_event	1000g_AF	1000g_max_AF	IMH_ID	IMH_AF	IMH_ID_others	promoters	dbVar_event	dbVar_variant	dbVar_status	TADcoordinates	ENCODEexperiments	GCcontent_left	GCcontent_right	Repeats_coord_left	Repeats_type_left	Repeats_coord_right	Repeats_type_right	ACMG	delZ_ExAC	dupZ_ExAC	cnvZ_ExAC	synZ_ExAC	misZ_ExAC	pLI_ExAC	HI_CGscore	TriS_CGscore	HI_DDDpercent	DDD_status	DDD_mode	DDD_consequence	DDD_disease	DDD_pmids	Phenotypes	Inheritance	morbidGenes	morbidGenesCandidates	Mim Number	AnnotSV ranking
AnnotSV ID	SV chrom	SV start	SV end	SV length	SV type	ID	REF	ALT	QUAL	FILTER	INFO	AnnotSV type	Gene name	NM	CDS length	tx length	location	location2	intersectStart	intersectEnd	DGV_GAIN_IDs	DGV_GAIN_n_samples_with_SV	DGV_GAIN_n_samples_tested	DGV_GAIN_Frequency	DGV_LOSS_IDs	DGV_LOSS_n_samples_with_SV	DGV_LOSS_n_samples_tested	DGV_LOSS_Frequency	GD_ID	GD_AN	GD_N_HET	GD_N_HOMALT	GD_AF	GD_POPMAX_AF	GD_ID_others	1000g_event	1000g_AF	1000g_max_AF	IMH_ID	IMH_AF	IMH_ID_others	promoters	dbVar_event	dbVar_variant	dbVar_status	TADcoordinates	ENCODEexperiments	GCcontent_left	GCcontent_right	Repeats_coord_left	Repeats_type_left	Repeats_coord_right	Repeats_type_right	ACMG	delZ_ExAC	dupZ_ExAC	cnvZ_ExAC	synZ_ExAC	misZ_ExAC	pLI_ExAC	Mim Number	Phenotypes	Inheritance	morbidGenesCandidates	morbidGenes	HI_CGscore	TriS_CGscore	DDD_status	DDD_mode	DDD_consequence	DDD_disease	DDD_pmids	HI_DDDpercent	AnnotSV ranking

I'll try to debug it, but for now we have 5 runs with same results on each machine (same for machine but not between different machines) and I don't see any reason for it. Maybe you know anything that can cause such behavior?

In-frame / out-frame annotation

I am working with WES-based CNV calls and a lot of them are intragenic CNVs. I want to prioritize intragenic duplications and analyze only those, which are out-of-frame and may result in frameshift effect.
Is it possible to add annotation regarding in-frame and out-frame exons to the AnnotSV annotations that can be used for intragenic CNVs?

Best,
Dmitrijs

Cytoband annotation feature to AnnotSV please.

#Version 3.0
For large SV annotation, can we add cytoband annotation feature to AnnotSV ? Please see here WGLab/doc-ANNOVAR#144.

Bug with the "candidateGenesFiltering" option

Hi Veronique

First of all, Thanks a lot for creating such wonderful tool. It's really helpful and time-saver in annonation process.
I have a query regarding annotation mode output.

I am annotating a VCF file in default Annotation mode (values : both as default)

Most of the SVs have two entries as "Full" and "Split".
but, some SVs only have "split" annotated mode entries.

Can you please check if there's some bug or i am missing some attribute in Annotation ?

Thanks in advance

ACMG 2019 Criteria

Have you planned to update your SV ranking according to the 2019 ACMG Criteria?
Thanks!

Calculation of SV_start and SV_length

Hi,

I'm having trouble understanding how SV_start and SV_length are calculated in AnnotSV. The values for these fields do not match the POS from my input VCF or any INFO fields. Similarly I have a similar issue with SV_length.

Below is a concise example to illustrate the issue - happy to rprovide more details if needed.

AnnotSV command:
./bin/AnnotSV -SVinputFile $INPUT -outputFile $OUTPUT

Input VCF fields:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
1	1866309	.	T		.	PASS	AC=1;AN=2;CIEND=-604,29;CIEND95=-108,7;CIGAR=1M1I396D;CIPOS=-30,458;CIPOS95=-5,96;DOWNSTREAM_PAIR_COUNT=0;END=1867025;IMPRECISE;NUM_SVMETHODS=2;NUM_SVTOOLS=2;PAIR_COUNT=0;PE=8;PREND=6.18918e-24,1.45446e-23,2.41556e-23,4.30094e-23,5.91275e-23,8.69823e-23,1.21355e-22,1.70497e-22,2.30798e-22,2.87843e-22,3.66785e-22,4.54739e-22,5.65922e-22,6.90145e-22,8.24203e-22,1.02715e-21,1.23778e-21,1.53537e-21,1.87795e-21,2.31809e-21,2.82447e-21,3.40671e-21,4.12499e-21,4.90559e-21,5.71953e-21,6.88336e-21,8.1121e-21,9.54805e-21,1.1343e-20,1.3186e-20,1.54438e-20,1.81284e-20,2.11144e-20,2.48403e-20,2.88384e-20,3.40288e-20,3.94195e-20,4.62168e-20,5.46624e-20,6.46865e-20,7.41941e-20,8.58379e-20,1.00421e-19,1.15106e-19,1.33155e-19,1.54014e-19,1.76869e-19,2.06731e-19,2.38539e-19,2.74132e-19,3.18003e-19,3.64535e-19,4.22231e-19,4.89845e-19,5.60432e-19,6.49272e-19,7.49182e-19,8.59873e-19,9.79117e-19,1.12971e-18,1.28173e-18,1.46975e-18,1.68169e-18,1.9251e-18,2.21203e-18,2.52183e-18,2.89453e-18,3.31063e-18,3.78542e-18,4.33792e-18,4.97503e-18,5.66079e-18,6.45949e-18,7.35856e-18,8.39344e-18,9.54484e-18,1.07713e-17,1.21978e-17,1.38224e-17,1.57601e-17,1.77685e-17,2.0158e-17,2.28296e-17,2.60735e-17,2.96202e-17,3.34976e-17,3.7979e-17,4.26591e-17,4.85151e-17,5.46692e-17,6.2068e-17,7.02881e-17,7.93499e-17,8.97437e-17,1.01506e-16,1.14539e-16,1.28553e-16,1.45085e-16,1.63151e-16,1.83061e-16,2.05676e-16,2.32536e-16,2.61261e-16,2.94709e-16,3.32053e-16,3.72896e-16,4.20622e-16,4.71314e-16,5.32245e-16,5.94096e-16,6.68293e-16,7.49352e-16,8.40348e-16,9.44991e-16,1.06487e-15,1.19581e-15,1.3371e-15,1.50072e-15,1.67717e-15,1.86708e-15,2.09178e-15,2.33964e-15,2.60598e-15,2.91844e-15,3.25867e-15,3.63862e-15,4.09244e-15,4.56453e-15,5.12395e-15,5.72234e-15,6.38735e-15,7.12326e-15,7.95832e-15,8.89455e-15,9.92108e-15,1.10839e-14,1.2327e-14,1.37372e-14,1.53693e-14,1.70532e-14,1.89844e-14,2.11768e-14,2.35433e-14,2.61622e-14,2.91258e-14,3.24467e-14,3.61578e-14,4.03381e-14,4.49189e-14,4.99501e-14,5.55941e-14,6.15892e-14,6.85588e-14,7.61918e-14,8.45455e-14,9.37589e-14,1.03806e-13,1.15309e-13,1.27988e-13,1.41643e-13,1.56732e-13,1.7396e-13,1.92822e-13,2.14037e-13,2.37328e-13,2.6225e-13,2.89932e-13,3.20621e-13,3.56328e-13,3.94844e-13,4.37454e-13,4.83088e-13,5.34516e-13,5.9065e-13,6.51617e-13,7.1965e-13,7.97122e-13,8.7989e-13,9.69381e-13,1.06941e-12,1.18012e-12,1.30059e-12,1.43409e-12,1.5851e-12,1.74492e-12,1.92084e-12,2.11911e-12,2.33377e-12,2.57331e-12,2.83423e-12,3.12725e-12,3.44193e-12,3.78163e-12,4.16897e-12,4.57697e-12,5.03765e-12,5.54139e-12,6.08633e-12,6.67861e-12,7.3381e-12,8.06527e-12,8.86289e-12,9.7461e-12,1.07124e-11,1.17395e-11,1.28893e-11,1.41223e-11,1.54517e-11,1.69429e-11,1.86217e-11,2.03918e-11,2.23911e-11,2.45211e-11,2.6928e-11,2.95201e-11,3.23246e-11,3.54366e-11,3.87753e-11,4.24158e-11,4.65639e-11,5.09983e-11,5.57779e-11,6.09606e-11,6.67314e-11,7.29853e-11,8.0013e-11,8.73945e-11,9.53842e-11,1.04095e-10,1.13835e-10,1.24266e-10,1.3564e-10,1.48172e-10,1.61888e-10,1.76896e-10,1.93074e-10,2.10557e-10,2.2974e-10,2.50783e-10,2.73734e-10,2.98361e-10,3.25435e-10,3.53991e-10,3.8546e-10,4.2035e-10,4.5831e-10,4.99398e-10,5.43752e-10,5.92131e-10,6.44592e-10,7.006e-10,7.61503e-10,8.29289e-10,9.01808e-10,9.81016e-10,1.06683e-09,1.15862e-09,1.25899e-09,1.36666e-09,1.48662e-09,1.61129e-09,1.75305e-09,1.90274e-09,2.06495e-09,2.24404e-09,2.43779e-09,2.64199e-09,2.86749e-09,3.10554e-09,3.36543e-09,3.64834e-09,3.96016e-09,4.29327e-09,4.64762e-09,5.03299e-09,5.46266e-09,5.90802e-09,6.39698e-09,6.92548e-09,7.49933e-09,8.10457e-09,8.78279e-09,9.48067e-09,1.02546e-08,1.10846e-08,1.19796e-08,1.29573e-08,1.40162e-08,1.51306e-08,1.63408e-08,1.7626e-08,1.90534e-08,2.05506e-08,2.21535e-08,2.39124e-08,2.58099e-08,2.78516e-08,3.00132e-08,3.2356e-08,3.48796e-08,3.75828e-08,4.0485e-08,4.35775e-08,4.6929e-08,5.05191e-08,5.4412e-08,5.85779e-08,6.30525e-08,6.77985e-08,7.29521e-08,7.84719e-08,8.43015e-08,9.06381e-08,9.73846e-08,1.04717e-07,1.12499e-07,1.20872e-07,1.29817e-07,1.39296e-07,1.49436e-07,1.60458e-07,1.72123e-07,1.84499e-07,1.98179e-07,2.12586e-07,2.28084e-07,2.44576e-07,2.61897e-07,2.80749e-07,3.0106e-07,3.22649e-07,3.45611e-07,3.70072e-07,3.96174e-07,4.2402e-07,4.53489e-07,4.85107e-07,5.19467e-07,5.5529e-07,5.94291e-07,6.35502e-07,6.79317e-07,7.26647e-07,7.77019e-07,8.30413e-07,8.8745e-07,9.4892e-07,1.01286e-06,1.08099e-06,1.15395e-06,1.23095e-06,1.31376e-06,1.40119e-06,1.49498e-06,1.59242e-06,1.69737e-06,1.80885e-06,1.92795e-06,2.05529e-06,2.18858e-06,2.33086e-06,2.47968e-06,2.64095e-06,2.80928e-06,2.98914e-06,3.18115e-06,3.38512e-06,3.60045e-06,3.82596e-06,4.06377e-06,4.3182e-06,4.59365e-06,4.87779e-06,5.18118e-06,5.49866e-06,5.83608e-06,6.19395e-06,6.57357e-06,6.97266e-06,7.39573e-06,7.84675e-06,8.32349e-06,8.8232e-06,9.35086e-06,9.90933e-06,1.05068e-05,1.11304e-05,1.17939e-05,1.24894e-05,1.32125e-05,1.39841e-05,1.47943e-05,1.56477e-05,1.65562e-05,1.75013e-05,1.84988e-05,1.95583e-05,2.0673e-05,2.1841e-05,2.30751e-05,2.43631e-05,2.57333e-05,2.71643e-05,2.86796e-05,3.025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AnnotSV output:

AnnotSV_ID	SV_chrom	SV_start	SV_end	SV_length	SV_type	Samples_ID	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1	Annotation_mode	Gene_name	Gene_count	Tx	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	P_snvindel_nb	P_snvindel_phen	B_gain_source	B_gain_coord	B_loss_source	B_loss_coord	B_ins_source	B_ins_coord	B_inv_source	B_inv_coord	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	ACMG	HI	TS	DDD_HI_percent	DDD_status	DDD_mode	DDD_consequence	DDD_disease	DDD_pmid	ExAC_delZ	ExAC_dupZ	ExAC_cnvZ	ExAC_synZ	ExAC_misZ	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
1_1866279_1867054_DEL_1	1	1866279	1867054	-649	DEL	Sample1	.	T		.	PASS	AC=1;AN=2;CIEND=-604,29;CIEND95=-108,7;CIGAR=1M1I396D;CIPOS=-30,458;CIPOS95=-5,96;DOWNSTREAM_PAIR_COUNT=0;END=1867025;IMPRECISE;NUM_SVMETHODS=2;NUM_SVTOOLS=2;PAIR_COUNT=0;PE=8;PREND=6.18918e-24,1.45446e-23,2.41556e-23,4.30094e-23,5.91275e-23,8.69823e-23,1.21355e-22,1.70497e-22,2.30798e-22,2.87843e-22,3.66785e-22,4.54739e-22,5.65922e-22,6.90145e-22,8.24203e-22,1.02715e-21,1.23778e-21,1.53537e-21,1.87795e-21,2.31809e-21,2.82447e-21,3.40671e-21,4.12499e-21,4.90559e-21,5.71953e-21,6.88336e-21,8.1121e-21,9.54805e-21,1.1343e-20,1.3186e-20,1.54438e-20,1.81284e-20,2.11144e-20,2.48403e-20,2.88384e-20,3.40288e-20,3.94195e-20,4.62168e-20,5.46624e-20,6.46865e-20,7.41941e-20,8.58379e-20,1.00421e-19,1.15106e-19,1.33155e-19,1.54014e-19,1.76869e-19,2.06731e-19,2.38539e-19,2.74132e-19,3.18003e-19,3.64535e-19,4.22231e-19,4.89845e-19,5.60432e-19,6.49272e-19,7.49182e-19,8.59873e-19,9.79117e-19,1.12971e-18,1.28173e-18,1.46975e-18,1.68169e-18,1.9251e-18,2.21203e-18,2.52183e-18,2.89453e-18,3.31063e-18,3.78542e-18,4.33792e-18,4.97503e-18,5.66079e-18,6.45949e-18,7.35856e-18,8.39344e-18,9.54484e-18,1.07713e-17,1.21978e-17,1.38224e-17,1.57601e-17,1.77685e-17,2.0158e-17,2.28296e-17,2.60735e-17,2.96202e-17,3.34976e-17,3.7979e-17,4.26591e-17,4.85151e-17,5.46692e-17,6.2068e-17,7.02881e-17,7.93499e-17,8.97437e-17,1.01506e-16,1.14539e-16,1.28553e-16,1.45085e-16,1.63151e-16,1.83061e-16,2.05676e-16,2.32536e-16,2.61261e-16,2.94709e-16,3.32053e-16,3.72896e-16,4.20622e-16,4.71314e-16,5.32245e-16,5.94096e-16,6.68293e-16,7.49352e-16,8.40348e-16,9.44991e-16,1.06487e-15,1.19581e-15,1.3371e-15,1.50072e-15,1.67717e-15,1.86708e-15,2.09178e-15,2.33964e-15,2.60598e-15,2.91844e-15,3.25867e-15,3.63862e-15,4.09244e-15,4.56453e-15,5.12395e-15,5.72234e-15,6.38735e-15,7.12326e-15,7.95832e-15,8.89455e-15,9.92108e-15,1.10839e-14,1.2327e-14,1.37372e-14,1.53693e-14,1.70532e-14,1.89844e-14,2.11768e-14,2.35433e-14,2.61622e-14,2.91258e-14,3.24467e-14,3.61578e-14,4.03381e-14,4.49189e-14,4.99501e-14,5.55941e-14,6.15892e-14,6.85588e-14,7.61918e-14,8.45455e-14,9.37589e-14,1.03806e-13,1.15309e-13,1.27988e-13,1.41643e-13,1.56732e-13,1.7396e-13,1.92822e-13,2.14037e-13,2.37328e-13,2.6225e-13,2.89932e-13,3.20621e-13,3.56328e-13,3.94844e-13,4.37454e-13,4.83088e-13,5.34516e-13,5.9065e-13,6.51617e-13,7.1965e-13,7.97122e-13,8.7989e-13,9.69381e-13,1.06941e-12,1.18012e-12,1.30059e-12,1.43409e-12,1.5851e-12,1.74492e-12,1.92084e-12,2.11911e-12,2.33377e-12,2.57331e-12,2.83423e-12,3.12725e-12,3.44193e-12,3.78163e-12,4.16897e-12,4.57697e-12,5.03765e-12,5.54139e-12,6.08633e-12,6.67861e-12,7.3381e-12,8.06527e-12,8.86289e-12,9.7461e-12,1.07124e-11,1.17395e-11,1.28893e-11,1.41223e-11,1.54517e-11,1.69429e-11,1.86217e-11,2.03918e-11,2.23911e-11,2.45211e-11,2.6928e-11,2.95201e-11,3.23246e-11,3.54366e-11,3.87753e-11,4.24158e-11,4.65639e-11,5.09983e-11,5.57779e-11,6.09606e-11,6.67314e-11,7.29853e-11,8.0013e-11,8.73945e-11,9.53842e-11,1.04095e-10,1.13835e-10,1.24266e-10,1.3564e-10,1.48172e-10,1.61888e-10,1.76896e-10,1.93074e-10,2.10557e-10,2.2974e-10,2.50783e-10,2.73734e-10,2.98361e-10,3.25435e-10,3.53991e-10,3.8546e-10,4.2035e-10,4.5831e-10,4.99398e-10,5.43752e-10,5.92131e-10,6.44592e-10,7.006e-10,7.61503e-10,8.29289e-10,9.01808e-10,9.81016e-10,1.06683e-09,1.15862e-09,1.25899e-09,1.36666e-09,1.48662e-09,1.61129e-09,1.75305e-09,1.90274e-09,2.06495e-09,2.24404e-09,2.43779e-09,2.64199e-09,2.86749e-09,3.10554e-09,3.36543e-09,3.64834e-09,3.96016e-09,4.29327e-09,4.64762e-09,5.03299e-09,5.46266e-09,5.90802e-09,6.39698e-09,6.92548e-09,7.49933e-09,8.10457e-09,8.78279e-09,9.48067e-09,1.02546e-08,1.10846e-08,1.19796e-08,1.29573e-08,1.40162e-08,1.51306e-08,1.63408e-08,1.7626e-08,1.90534e-08,2.05506e-08,2.21535e-08,2.39124e-08,2.58099e-08,2.78516e-08,3.00132e-08,3.2356e-08,3.48796e-08,3.75828e-08,4.0485e-08,4.35775e-08,4.6929e-08,5.05191e-08,5.4412e-08,5.85779e-08,6.30525e-08,6.77985e-08,7.29521e-08,7.84719e-08,8.43015e-08,9.06381e-08,9.73846e-08,1.04717e-07,1.12499e-07,1.20872e-07,1.29817e-07,1.39296e-07,1.49436e-07,1.60458e-07,1.72123e-07,1.84499e-07,1.98179e-07,2.12586e-07,2.28084e-07,2.44576e-07,2.61897e-07,2.80749e-07,3.0106e-07,3.22649e-07,3.45611e-07,3.70072e-07,3.96174e-07,4.2402e-07,4.53489e-07,4.85107e-07,5.19467e-07,5.5529e-07,5.94291e-07,6.35502e-07,6.79317e-07,7.26647e-07,7.77019e-07,8.30413e-07,8.8745e-07,9.4892e-07,1.01286e-06,1.08099e-06,1.15395e-06,1.23095e-06,1.31376e-06,1.40119e-06,1.49498e-06,1.59242e-06,1.69737e-06,1.80885e-06,1.92795e-06,2.05529e-06,2.18858e-06,2.33086e-06,2.47968e-06,2.64095e-06,2.80928e-06,2.98914e-06,3.18115e-06,3.38512e-06,3.60045e-06,3.82596e-06,4.06377e-06,4.3182e-06,4.59365e-06,4.87779e-06,5.18118e-06,5.49866e-06,5.83608e-06,6.19395e-06,6.57357e-06,6.97266e-06,7.39573e-06,7.84675e-06,8.32349e-06,8.8232e-06,9.35086e-06,9.90933e-06,1.05068e-05,1.11304e-05,1.17939e-05,1.24894e-05,1.32125e-05,1.39841e-05,1.47943e-05,1.56477e-05,1.65562e-05,1.75013e-05,1.84988e-05,1.95583e-05,2.0673e-05,2.1841e-05,2.30751e-05,2.43631e-05,2.57333e-05,2.71643e-05,2.86796e-05,3.025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(1 gene);5F	3
1_1866279_1867054_DEL_1	1	1866279	1867054	-649	DEL	Sample1	.	T		.	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23521e-05,4.04056e-05,3.85276e-05,3.67376e-05,3.49989e-05,3.33312e-05,3.17368e-05,3.02164e-05,2.87945e-05,2.74103e-05,2.60851e-05,2.48426e-05,2.36211e-05,2.24603e-05,2.13483e-05,2.03006e-05,1.92732e-05,1.83201e-05,1.74077e-05,1.65038e-05,1.56849e-05,1.49058e-05,1.4135e-05,1.342e-05,1.27329e-05,1.20644e-05,1.14307e-05,1.08296e-05,1.02617e-05,9.73413e-06,9.22253e-06,8.7292e-06,8.26726e-06,7.82679e-06,7.41356e-06,7.02265e-06,6.65234e-06,6.28102e-06,5.93646e-06,5.61703e-06,5.30985e-06,5.02208e-06,4.74883e-06,4.48679e-06,4.2448e-06,4.01229e-06,3.78353e-06,3.57429e-06,3.36732e-06,3.17641e-06,2.99645e-06,2.82656e-06,2.66336e-06,2.5125e-06,2.36773e-06,2.22972e-06,2.09884e-06,1.97632e-06,1.85883e-06,1.74954e-06,1.64786e-06,1.54971e-06,1.45624e-06,1.36778e-06,1.28579e-06,1.20811e-06,1.1368e-06,1.06762e-06,1.00328e-06,9.43172e-07,8.84267e-07,8.27628e-07,7.76472e-07,7.29816e-07,6.85126e-07,6.41551e-07,6.00743e-07,5.63286e-07,5.28084e-07,4.95247e-07,4.64125e-07,4.33584e-07,4.0637e-07,3.79492e-07,3.54895e-07,3.31706e-07,3.10452e-07,2.89975e-07,2.70085e-07,2.52294e-07,2.35759e-07,2.20009e-07,2.05584e-07,1.9219e-07,1.7912e-07,1.67036e-07,1.55842e-07,1.45091e-07,1.35116e-07,1.25834e-07,1.17385e-07,1.09235e-07,1.01693e-07,9.43218e-08,8.76705e-08,8.15687e-08,7.5786e-08,7.04065e-08,6.55164e-08,6.07776e-08,5.62545e-08,5.23594e-08,4.87259e-08,4.51737e-08,4.20113e-08,3.90184e-08,3.61671e-08,3.35483e-08,3.10467e-08,2.87576e-08,2.66863e-08,2.46845e-08,2.28188e-08,2.11474e-08,1.95542e-08,1.80696e-08,1.67165e-08,1.5478e-08,1.43032e-08,1.3238e-08,1.22579e-08,1.13119e-08,1.05013e-08,9.69615e-09,8.95688e-09,8.2743e-09,7.63577e-09,7.04807e-09,6.50273e-09,5.98462e-09,5.51806e-09,5.08759e-09,4.69471e-09,4.29832e-09,3.96584e-09,3.645e-09,3.36457e-09,3.10529e-09,2.84875e-09,2.61766e-09,2.40858e-09,2.21629e-09,2.04444e-09,1.87708e-09,1.72334e-09,1.58402e-09,1.45089e-09,1.32741e-09,1.21724e-09,1.12071e-09,1.02776e-09,9.41076e-10,8.63049e-10,7.9149e-10,7.29655e-10,6.70495e-10,6.1292e-10,5.59457e-10,5.12794e-10,4.69343e-10,4.27341e-10,3.91673e-10,3.57899e-10,3.27071e-10,2.98231e-10,2.73822e-10,2.50098e-10,2.28582e-10,2.08691e-10,1.90088e-10,1.73631e-10,1.58079e-10,1.43982e-10,1.3074e-10,1.19833e-10,1.08759e-10,9.94112e-11,9.0464e-11,8.16033e-11,7.4184e-11,6.74656e-11,6.15496e-11,5.5816e-11,5.08762e-11,4.60501e-11,4.18147e-11,3.79331e-11,3.4335e-11,3.10796e-11,2.80557e-11,2.53902e-11,2.29093e-11,2.07266e-11,1.87647e-11,1.68817e-11,1.52962e-11,1.38206e-11,1.2484e-11,1.1325e-11,1.02103e-11,9.19008e-12,8.36432e-12,7.51353e-12,6.76906e-12,6.07819e-12,5.45734e-12,4.86125e-12,4.38722e-12,3.92597e-12,3.56096e-12,3.22696e-12,2.87667e-12,2.5893e-12,2.33053e-12,2.08791e-12,1.87876e-12,1.68335e-12,1.51396e-12,1.36095e-12,1.21217e-12,1.09612e-12,9.85663e-13,8.70904e-13,7.65585e-13,6.7771e-13,6.08667e-13,5.41294e-13,4.8176e-13,4.2815e-13,3.78906e-13,3.3469e-13,2.9918e-13,2.68169e-13,2.37898e-13,2.11009e-13,1.87001e-13,1.62514e-13,1.44765e-13,1.26115e-13,1.09411e-13,9.51086e-14,8.04249e-14,6.86328e-14,5.98173e-14,5.07854e-14,4.39242e-14,3.70856e-14,3.2612e-14,2.80873e-14,2.39014e-14,2.04528e-14,1.68952e-14,1.41742e-14,1.1171e-14,8.471e-15,6.39333e-15,4.73323e-15,3.58913e-15,2.15841e-15,1.39551e-15;RO_BESTHIT=.;RO_BHLENGTH=704;RO_LENGTH=717;RO_NHITS=1;RO_OVERLAP=0.982;RO_OVERLAPLENGTH=704;SOURCES=1-1866309-1-1866705-396-Manta,1-1866376-1-1867025-649-Lumpy;SR=0;STRANDS=+-:8;SU=8;SVLEN=-649;SVMETHOD=RP,SR;SVTOOL=MetaSV;SVTYPE=DEL;UPSTREAM_PAIR_COUNT=0;VT=SV;GCF=0.496513	GT:DHFC:DHFFC:DHBFC:DHSP	1/1:0.368421:0.378378:0.388889:14	split	CFAP74		NM_001304360	1853395	1935225	775	0	0	no	39	intron25-intron25	CDS	3239	5'	1866279	1867054																																											91.8																					full=3

Expected start, end and length:

CHROM	START	END	LENGTH
1	1866309	1867025	717

Note: my input VCF file was generated using MetaSV from Lumpy and Manta data.

Any advice you can offer would be much appreciated.

Version AnnotSV 2.4

Dear all,

in the changeLog.txt appear a new version of AnnotSV 2.4, is avaliable if we git clone the repository as describe in the Readme file? I mention this beacuse is confused which version is the lastest one... some files are named as 2.3.2 and for example the changeLog.txt appear this new version from July month...

Thanks for your help

Jordi

Custom PREFIX in make install

Hello.
We are trying to install your tool, and we have common practice to not installing tools in same directory where sources are located.
According to your Makefile we can do it: https://github.com/lgmgeo/AnnotSV/blob/master/Makefile#L60

But we're getting some errors:

root@d8a20fd62387:/soft/AnnotSV-8b19c75bab990190715ba5a7d9afa164e8b9c7d5# make PREFIX="$SOFT/AnnotSV-${ANNOTSV_VERSION}" install

Installation of AnnotSV-2.3.2:
----------------------------
DESTDIR=
PREFIX=/soft/AnnotSV-2.3.2
TCLVERSION=tcl8.6

Configfile configuration
------------------------
install -d /soft/AnnotSV-2.3.2/etc/AnnotSV
install -p -m 0755 etc/AnnotSV/configfile  /soft/AnnotSV-2.3.2/etc/AnnotSV

Makefile installation
---------------------
install -p -m 0755 Makefile  /soft/AnnotSV-2.3.2

Executable installation
-----------------------
install -d /soft/AnnotSV-2.3.2/bin
install -p -m 0755 bin/AnnotSV /soft/AnnotSV-2.3.2/bin

Tcl scripts installation
------------------------
install -d /soft/AnnotSV-2.3.2/share/tcl8.6/AnnotSV
install -p -m 0644 share/tcl/AnnotSV/AnnotSV-1000g.tcl share/tcl/AnnotSV/AnnotSV-gccontent.tcl share/tcl/AnnotSV/AnnotSV-genehancer.tcl share/tcl/AnnotSV/AnnotSV-exac.tcl share/tcl/AnnotSV/AnnotSV-config.tcl share/tcl/AnnotSV/AnnotSV-userBED.tcl share/tcl/AnnotSV/AnnotSV-dgv.tcl share/tcl/AnnotSV/AnnotSV-ranking.tcl
 share/tcl/AnnotSV/AnnotSV-pathogenic-NR-SV.tcl share/tcl/AnnotSV/AnnotSV-help.tcl share/tcl/AnnotSV/AnnotSV-haploinsufficiency.tcl share/tcl/AnnotSV/AnnotSV-vcf.tcl share/tcl/AnnotSV/AnnotSV-imh.tcl share/tcl/AnnotSV/AnnotSV-gnomad.tcl share/tcl/AnnotSV/AnnotSV-ddd.tcl share/tcl/AnnotSV/AnnotSV-promoter.tcl share/t
cl/AnnotSV/AnnotSV-tad.tcl share/tcl/AnnotSV/AnnotSV-exomiser.tcl share/tcl/AnnotSV/AnnotSV-clingen.tcl share/tcl/AnnotSV/AnnotSV-extann.tcl share/tcl/AnnotSV/AnnotSV-repeat.tcl share/tcl/AnnotSV/AnnotSV-general.tcl share/tcl/AnnotSV/AnnotSV-filteredVCF.tcl share/tcl/AnnotSV/AnnotSV-refGene.tcl share/tcl/AnnotSV/Ann
otSV-write.tcl share/tcl/AnnotSV/AnnotSV-omim.tcl share/tcl/AnnotSV/tcllib/tar/tar.tcl share/tcl/AnnotSV/tcllib/tar/pkgIndex.tcl share/tcl/AnnotSV/tcllib/http/pkgIndex.tcl share/tcl/AnnotSV/tcllib/http/autoproxy.tcl share/tcl/AnnotSV/tcllib/json/json_tcl.tcl share/tcl/AnnotSV/tcllib/json/json_write.tcl share/tcl/Ann
otSV/tcllib/json/pkgIndex.tcl share/tcl/AnnotSV/tcllib/json/jsonc.tcl share/tcl/AnnotSV/tcllib/json/json.tcl share/tcl/AnnotSV/tcllib/csv/csv.tcl share/tcl/AnnotSV/tcllib/csv/pkgIndex.tcl /soft/AnnotSV-2.3.2/share/tcl8.6/AnnotSV
install: will not overwrite just-created '/soft/AnnotSV-2.3.2/share/tcl8.6/AnnotSV/pkgIndex.tcl' with 'share/tcl/AnnotSV/tcllib/http/pkgIndex.tcl'
install: will not overwrite just-created '/soft/AnnotSV-2.3.2/share/tcl8.6/AnnotSV/pkgIndex.tcl' with 'share/tcl/AnnotSV/tcllib/json/pkgIndex.tcl'
install: will not overwrite just-created '/soft/AnnotSV-2.3.2/share/tcl8.6/AnnotSV/pkgIndex.tcl' with 'share/tcl/AnnotSV/tcllib/csv/pkgIndex.tcl'
Makefile:100: recipe for target 'install-tcl-toolbox' failed
make: *** [install-tcl-toolbox] Error 1

The reason is copying several files with exact same basename pkgIndex.tcl into one directory here. Can you fix this please?

Annotation for other genome

Hi，
I have installed AnnotSV to annotate my own SV data. My study is about peach. So can this tool be used for peach? How could I build the genome? Because the default is human genome.
Cheers,
Jian

Can I turn off the "pathogenic/benign SV annotation" mode?

Hi, THANKS a lot for providing this great tool for SV annotation.

The latest version (December 19, 2020: AnnotSV 3.0 is alive!) updated:

Merge pathogenic SV annotation (from multiple sources)
Merge benign SV annotation (from multiple sources)

and Remove previous annotation columns from DDD, DGV, gnomAD, 1000g and IMH

Allele Frequency seems to be a good filter item, but it can't be found now. (sad)

hg38 annotation fail

dear Igmeo, many thanks for creating AnnotSV!

i was trying to install AnnotSV and annotate SV with hg38 data, however, the following message came up on first run:
WARNING: X, format (nb columns) is not good 89 vs 0 columns
WARNING: Reading Annotation file 20201208_gnomAD.LOEUF.pLI.annotations.tsv and X is seen multiple times.
WARNING: X, format (nb columns) is not good 89 vs 0 columns
...
WARNING: Y, format (nb columns) is not good 89 vs 0 columns
WARNING: Reading Annotation file 20201208_gnomAD.LOEUF.pLI.annotations.tsv and Y is seen multiple times.

...listing of the annotations to realized (December 09 2020 - 13:17)
...Genes annotation
(with share/AnnotSV/Annotations_Human/Genes/GRCh38/genes.RefSeq.sorted.bed)
...Genes-based annotations
...20201204_ClinGenAnnotations.tsv.gz
(1129 gene identifiers and 2 annotations columns: HI_CGscore, TriS_CGscore)
...20201204_HI.tsv.gz
(19124 gene identifiers and 1 annotations columns: HI_DDDpercent)
...20201208_ExAC.CNV-Zscore.annotations.tsv.gz
(15673 gene identifiers and 3 annotations columns: delZ_ExAC, dupZ_ExAC, cnvZ_ExAC)
...20201208_GeneIntolerance-Zscore.annotations.tsv.gz
(18241 gene identifiers and 2 annotations columns: synZ_ExAC, misZ_ExAC)
...20201204_OMIM-1-annotations.tsv.gz
(15004 gene identifiers and 1 annotations columns: Mim Number)
...20201204_OMIM-2-annotations.tsv.gz
(15004 gene identifiers and 2 annotations columns: Phenotypes, Inheritance)
...20201204_morbidGenes.tsv.gz
(11845 gene identifiers and 1 annotations columns: morbidGenes)
...20201204_morbidGenesCandidates.tsv.gz
(3207 gene identifiers and 1 annotations columns: morbidGenesCandidates)
...20201208_gnomAD.LOEUF.pLI.annotations.tsv
(24 gene identifiers and -1 annotations columns: )
...Annotations with features overlapping the SV
...DGV Gold Standard frequency annotation
...1000g events annotation
...Annotations with features overlapped with the SV
...Promoters annotation
...Breakpoints annotations
...Repeat annotation
...Gap annotation
...Segmental duplication annotation
...ENCODE blacklist annotation

...annotation in progress (December 09 2020 - 13:17)
bad count "-1": must be integer >= 0
while executing
"lrepeat $nbColumns($F) """
(procedure "OrganizeAnnotation" line 843)
invoked from within
"OrganizeAnnotation"
(file "bin/AnnotSV" line 277)

is my annotation file not good?
why is the organization failing?
im trying to run it on a linux computer if that helps, do you need more info on that?

Thanks for your efforts in advance,
daaaaande

Can AnnotSV generate vcf-fomrat output?

Thank you.

Add HPO criteria and IDs to annotations

Would it be possible to add HPO criteria and their IDs to annotations?

Best regards.

Problem installaling AnnotSV

I am following the below steps to install AnnotSV and I encountered an error; find below the details

Downloaded the latest installer from this and unzipped using tar -zxvf AnnotSV_latest.tar.gz
Downloaded and installed tcsh

sudo apt-get install tcsh

Go to AnnotSV_2.2 folder and type below command:

make PREFIX=. install
/bin/mv License.txt changeLog.txt commandLineOptions.txt README.AnnotSV_2.2.pdf ./share/doc/AnnotSV
/bin/mv share/tcl ./share/tcl8.6
Done

Then at this command; I am facing this issue:

make PREFIX=. install-human-annotation
find: ‘share/tcl/AnnotSV/’: No such file or directory
make: *** No rule to make target 'install-human-annotation'.  Stop.

My folder structure look like this (after step#3)

├── bin
│   └── AnnotSV
├── etc
│   └── AnnotSV
├── Makefile
└── share
    ├── doc
    └── tcl8.6

Could you please help? I am using Ubuntu 16

lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.6 LTS
Release:	16.04
Codename:	xenial

-txFile option does not work

Could you please indicate how the user transcript file (-given after -txFile option) should be formatted?
I tried space delimited file and it does not work for me.
I use Ensembl based sorted.refGene.bed and Ensembl transcripts ids.
kt

Problem with -annotationMode split

Hello, I tried to run AnnotSV with the option -annotationMode split for the testcase in the repository. However, I got an error message as below. Do you have an idea what could cause this?

$ANNOTSV/bin/AnnotSV -annotationMode split -SVinputFile test.bed -outputFile ./test.annotated.tsv -svtBEDcol 4

Error message:

...annotation in progress (January 19 2021 - 10:19)

...writing of ./test.annotated.tsv (January 19 2021 - 10:19)
can't read "notSelected": no such variable
while executing
"if {$notSelected} {continue} "
(procedure "OrganizeAnnotation" line 1198)
invoked from within
"OrganizeAnnotation"
(file "/usr/src/app/AnnotSV/bin/AnnotSV" line 271)

Annotating MEIs, not seeing AnnotSV ranking

Hello,

I'm annotating a merged output from MELT, and I'm getting full annotations but not seeing any AnnotSV ranking scores or criteria.

I'm using the latest AnnotSV (3.0.7).

Thanks!
Phil

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lgmgeo / annotsv Goto Github PK

annotsv's Introduction

An integrated tool for Structural Variations annotation and ranking

Table of contents

AnnotSV Annotations Engine

AnnotSV Webserver

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annotsv's Issues

...writing of ./test.annotated.tsv (January 19 2021 - 10:19) can't read "notSelected": no such variable while executing "if {$notSelected} {continue} " (procedure "OrganizeAnnotation" line 1198) invoked from within "OrganizeAnnotation" (file "/usr/src/app/AnnotSV/bin/AnnotSV" line 271)

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Recommend Org

...writing of ./test.annotated.tsv (January 19 2021 - 10:19)
can't read "notSelected": no such variable
while executing
"if {$notSelected} {continue} "
(procedure "OrganizeAnnotation" line 1198)
invoked from within
"OrganizeAnnotation"
(file "/usr/src/app/AnnotSV/bin/AnnotSV" line 271)