Hello team GATK,
I have finished generating VCF files by following GATK best Practices documentation. And for some positions the AC and AF field have two values (Mostly Repetitive). Is it normal? If yes then how do I interpret it?
And If No then how do I get rid of such positions.
1473352 . C G,T 1769.77 PASS AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.590;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.47;MQRankSum=-0.599;QD=29.01;ReadPosRankSum=0.488;SOR=0.950 GT:AD:DP:GQ:PL 1/2:2,28,31:61:99:1798,738,1252,1106,0,1056