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how I interpret the genotype result?
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:
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.