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>