Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Variant Caller and BAM file INFO not matching
I am using gatk-126.96.36.199 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 ?