Error while converting VCF output file from ERDS using convert2annovar.pl program

Question

[bioinforesearchquestions]

Hi friends,

I am doing cnv calling using ERDS tool. ERDS provides a vcf file with cnv events. I would like to annotate the cnv events with gene level information. Therefore I am trying to use annovar to annotate the cnv events.

First step, I am converting the vcf from ERDS tool to annovar input format. So I used convert2annovar.pl program. I am getting the below error.

Did anybody face such an error with erds vcf conversion to annovar specific input?

$ perl annovar/convert2annovar.pl -format vcf4 sample1.erds.vcf > sample1.erds.avinput

Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chr1 10001="" .="" .="" <dup=""> . PASS IMPRECISE;SVTYPE=DUP;END=177000;SVLEN=167000 REFCN:CN 2:5>

Answer 1

[wyy_zsm]

Hi: I use stralka to call indels, and meet the same problem, does anyone can help ? thanks! /home/database/annovar/convert2annovar.pl -format vcf4 passed.somatic.indels.vcf >passed.somatic.indels.avinput WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead. Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chr20 44740487="" .="" gaa="" g="" .="" pass="" ic="0;IHP=3;NT=ref;QSI=31;QSI_NT=31;RC=2;RU=A;SGT=ref-">het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 5:5:5,5:0,0:0,0:4.04:0.00:0.00 26:26:2,3:24,26:0,0:22.79:0.00:0.00>