Hi,
We found this line in a VCF file and we're confused why GATK gave 1/1 when Ref has greater reads than Alt
chr10 5129483 . A C 49.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.152;DP=29; GT:AD:DP:GQ:PL 1/1:16,13:29:9:77,9,0
Is PL computed from filtered AD?
Thank you!