Hi there,
I am relatively new and working through stuff. I have looked around and high and low for an answer and could not find one. So here goes.
I am trying to use annovar to convert a VCF file for analysis. When I run convert2annovar.pl, I get the following error.
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chr3 41265950 . ATTCTTTT ATTTT 68.5 . INDEL;IS=10,0.072993;DP=136;VDB=7.627334e-21;AF1=0.5;AC1=1;DP4=8,5,2,20;MQ=44;FQ=68.9;PV4=0.0017,1,1,1 PL 106,0,107>
Needless to say, I examined my .vcf file and here is a field
chr3 41274764 . C A 222 . DP=4288;VDB=1.423052e-28;AF1=1;AC1=2;DP4=0,0,2246,2027;MQ=44;FQ=-282 PL 255,255,0
It is missing the "GT" tag.
My question is, at what step do I introduce the GT tag.
Is it with Bowtie alignment or Samtools mpileup or do I have to use separately vcftools to get the GT format in there?
I know this is a basic question, but I am trying to figure stuff out here. Thanks for the favor of a reply. I felt the vcf documentation was not quite clear about this.
I am relatively new and working through stuff. I have looked around and high and low for an answer and could not find one. So here goes.
I am trying to use annovar to convert a VCF file for analysis. When I run convert2annovar.pl, I get the following error.
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chr3 41265950 . ATTCTTTT ATTTT 68.5 . INDEL;IS=10,0.072993;DP=136;VDB=7.627334e-21;AF1=0.5;AC1=1;DP4=8,5,2,20;MQ=44;FQ=68.9;PV4=0.0017,1,1,1 PL 106,0,107>
Needless to say, I examined my .vcf file and here is a field
chr3 41274764 . C A 222 . DP=4288;VDB=1.423052e-28;AF1=1;AC1=2;DP4=0,0,2246,2027;MQ=44;FQ=-282 PL 255,255,0
It is missing the "GT" tag.
My question is, at what step do I introduce the GT tag.
Is it with Bowtie alignment or Samtools mpileup or do I have to use separately vcftools to get the GT format in there?
I know this is a basic question, but I am trying to figure stuff out here. Thanks for the favor of a reply. I felt the vcf documentation was not quite clear about this.
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