If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
AF calculation in Mutect2
I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel:
T057.mutect2.vcf:7 17379247 . CAACAGCAACAGTCCTTGGCTCTGAACTCAAGCTGTATGGTACAGGAACACCTACATCTAG C . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=57.68;TLOD=106.87 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:66,30:0.452:18:12:.:1983,919:32:34 0/0:214,0:0.112:0:0:.:6285,0:98:116
The tumour variant AF should be (30/(30+66)=0.31, but is reported as 0.42, while the normal variant AF should be 0/214=0, but is reported as 0.112
Am I missing something/misinterpreting these fields?
Any comments and help greatly appreciated!