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.