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PROBLEM IN VCF FILE: HALF GENOTYPE INFORMATION

anupamanupam Posts: 8Member
edited January 2013 in Ask the GATK team

Hi. I have converted the tsv file from Complete genomics(CGA tool) to vcf format. but, when I run programs, it says some error in my vcf format. I carefully examined the vcf file and found, in some SNVs the GT is 1|.(dot). Is it a valid vcf file or is there any problem in vcf file? The program showed the error in those lines in which GT is 1|.(dot) i.e half genotype information. The line looks like this:

1   55164   .   C   A   .   .   NS=1;AN=1;AC=1;CGA_XR=dbsnp.103|rs3091274;CGA_RPT=L2|L2|49.7;CGA_SDO=2  GT:PS:FT:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP  1/.:.:VQLOW:30,.:30,.:8,.:-30,0,0:-8,0,0:18:18,.:0
Post edited by Geraldine_VdAuwera on

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