left gene

[bioinfomatio]

Hi Why is the gene closest to it on the left side not ZNF384, but RP11-1038A11.1？The location is: 12:6800414

[lgmgeo]

Please detail your request when reporting a bug (AnnotSV version, command line, etc.)

I run:

$ANNOTSV/bin/AnnotSV -SVinputFile ./test.bed -outputFile ./test.annotated.tsv -svtbedcol 4 -tx ENSEMBL -genomeBuild GRCh37

with:

But I can't reproduced the bug, everything seems correct on my side:

Please, give me your command line and attach the VCF input file with your "12:6800414" translocation.

[bioinfomatio]

chr12 6800414 MantaBND:17297:0:1:0:0:0:0 C C]chr22:41540267] . PASS SVTYPE=BND;MATEID=MantaBND:17297:0:1:0:0:0:1;BND_DEPTH=122;MATE_BND_DEPTH=145 PR:SR 89,20:135,16

[bioinfomatio]

chr12 6800414 MantaBND:17297:0:1:0:0:0:0 C C]chr22:41540267] . PASS SVTYPE=BND;MATEID=MantaBND:17297:0:1:0:0:0:1;BND_DEPTH=122;MATE_BND_DEPTH=145 PR:SR 89,20:135,16 chr22 41540267 MantaBND:17297:0:1:0:0:0:1 A A]chr12:6800414] . PASS SVTYPE=BND;MATEID=MantaBND:17297:0:1:0:0:0:0;BND_DEPTH=145;MATE_BND_DEPTH=122 PR:SR 89,20:135,16

[bioinfomatio]

AnnotSV/3.4.2，The analysis result is RP11-1038A11.1, the correct result should be ZNF384

[lgmgeo]

Can you join the VCF input file in a new comment (in place of copy/paste)? This will save me from having to tab the VCF file myself and create a header.

[bioinfomatio]

fileformat=VCFv4.1

fileDate=20240625

source=GenerateSVCandidates 1.6.0

reference=file:////ucsc.hg19.fasta

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FORMAT=

FORMAT=0.999">

FILTER=

FILTER=

ALT=

ALT=

ALT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT WGS20240089

chr12 6800414 MantaBND:17297:0:1:0:0:0:0 C C]chr22:41540267] . PASS SVTYPE=BND;MATEID=MantaBND:17297:0:1:0:0:0:1;BND_DEPTH=122;MATE_BND_DEPTH=145 PR:SR 89,20:135,16 chr22 41540267 MantaBND:17297:0:1:0:0:0:1 A A]chr12:6800414] . PASS SVTYPE=BND;MATEID=MantaBND:17297:0:1:0:0:0:0;BND_DEPTH=145;MATE_BND_DEPTH=122 PR:SR 89,20:135,16

[lgmgeo]

Can you add this VCF file? (not paste)

[bioinfomatio]

[Uploading 6800414.v1.vcf.gz…]()

[lgmgeo]

Sorry, I can't reproduce your data.

I run AnnotSV 3.4.2 with test.vcf.gz:

$ANNOTSV/bin/AnnotSV -SVinputFile ./test.vcf.gz -outputFile ./test.annotated.tsv -tx ENSEMBL -genomeBuild GRCh37

And I obtained:

[bioinfomatio]

6800414.v1.vcf.gz

I gave you a new link, please check if you can download it.

[lgmgeo]

Same results

Did you run:

• The same command line?

  $ANNOTSV/bin/AnnotSV -SVinputFile ./6800414.v1.vcf -outputFile ./6800414.v1..annotated.tsv -tx ENSEMBL -genomeBuild GRCh37

• The same AnnotSV version? (3.4.2)

[bioinfomatio]

I repeated your code, but the result is still RP11-1038A11.1.

The reason for the different results may be that the /AnnotSV-3.4.2/share/AnnotSV/Annotations_Human/Genes/GRCh37/ genes.ensembl.sorted.bed file is different. Could you please upload the genes.ensembl.sorted.bed file?

Thank you so much

[bioinfomatio]

genes.ENSEMBL.sorted.zip

[lgmgeo]

Ok, by replacing your file in my install, I finally reproduced the bug. I get back to you asap

[lgmgeo]

You failed to indicate that you modified the genes.ENSEMBL.sorted.bed file yourself. And you did it wrong... This file needs to be sorted! You added 2 lines at the start of the file, unsorted:

I develop and maintain AnnotSV for free. I attach great importance to answering users' questions, even if it takes me a lot of time, so that this tool is useful to as many people as possible. So... As already mentioned, please detail your request when reporting a bug: - Give the version of AnnotSV and the command line used - Add/join the input file that allow to reproduce the bug - Give all the information that could have an impact on the bug reported (modifications made in the installation or in the annotation files)