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PROBLEM IN VCF FILE: HALF GENOTYPE INFORMATION

anupamanupam Member Posts: 8
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

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,371 admin

    Unfortunately we don't have the resources to provide support for this type of problem, which is not specific to GATK. Please see the VCF specification to understand what is wrong with your file or use VCF validation tools.

    Geraldine Van der Auwera, PhD

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