Hello,
I am using gatk-4.0.3.0 following the Best practices.
BWA-> Picard Mark Dup -> GATK Base Recalib/Apply -> HC variant calling per sample
For one of our samples, we have a variant called at 1:201021671:C/G The HC has the following info (relevant to us)
INFO-DP:569 FORMAT-AD:422,139 FORMAT-DP: 561 GQ:99
1 201021671 . C G 1543.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-13.710;ClippingRankSum=0.000;DP=569;ExcessHet=3.0103;FS=305.296;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.75;ReadPosRankSum=-4.819;SOR=9.883 GT:AD:DP:GQ:PL 0/1:422,139:561:99:1572,0,21081
But the BAM file in IGV shows something different for this variant
Total Count - 590,
AD Count - 574,11
Where does HC get a higher alternate count ? and why is the total count different ?
Thanks