how I interpret the genotype result?

love_boneslove_bones chinaMember
edited August 2016 in Ask the GATK team

Dear all,
Follow the GATK best practice, I got one sample with the genotype 0/0:47,0:49:99:0|1:131931451_TA_T:0,141,1807 in the vcf file. According to the format column GT:AD:DP:GQ:PGT:PID:PL, this item can be interpreted as:

GT: 0/0
AD: 47,0
DP: 49
GQ: 99
PGT:0|1
PID: 131931451_TA_T
PL:0,141,1807

I know the PGT and PID are new tags for physical phasing (http://gatkforums.broadinstitute.org/wdl/discussion/4682/pgt-and-pid-in-vcf). But I do not understand is why the GT(0/0) is not the same as the PGT(0|1).

The GATK version is 3.6-0-g89b7209.

Thanks.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @love_bones
    Hi,

    Can you please post IGV screenshots of the original BAM file and bamout file in the region? Please include the sites that are phased.

    Also, please post the exact VCF records of the two phased sites in question. The sites that are phased will have the same PID.

    -Sheila

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