Annotation of Pindel files using AnnotSV

Question

[biologist]

Hello everyone,

After running pindel on a tumor-normal paired sample, I used pind2vcf to create one vcf with all the pindel information contained. Then I used AnnotSV to annotate my vcf. The command looks like this:

$ANNOTSV/bin/AnnotSV -SVinputFile pindel.vcf -outputFile annotsv.vcf -txFile txFile

Somehow, in my AnnotSV output, I get a SV length of 1 for all events of type INS, INV and TandemDup although their SVLEN in the vcf' "INFO" column is longer than 1. Only Del shows the correct SV length that is reflected in the vcf's "INFO" column. Has anyone else encountered the same problem? This in turn shows wrong values for AnnotSV's column "IntersectEnd" and I am not sure if this impacts the column "location" which basically tells us which exon/intron this SV is taking place in.

Any suggestions as to improve my output would be appreciated.

Thanks

Answer 1

[LGMgeo]

Hi,

A bugfix has been added in AnnotSV, this SV length bad report should no longer be encountered. It's better to directly send an email to the author (me) for any bug that you can detect.

Otherwise, it is to notice that the AnnotSV output is a tsv file (tabulated separated values), not a VCF one.

Best regards