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.
How does MuTect2 assign germline_risk filter
I have read MuTect1 paper and MuTect2 code, and it seems the germline risk is assigned this way
1. if variants in dbsnp, but not cosmic, the nlod cutoff is 5.5
2. otherwise, the cutoff is 2.2
Some of the variants that looks like somatic, but are labelled as germline_risks, one example is
chr11 123456789 . C A . germline_risk ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=3.61;TLOD=12.81 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:13,0:0.00:0:0:.:440,0:10:3 0/1:10,6:0.357:2:4:0.667:336,173:4:6
And I used the MuTect2 default settings initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=
6.3 normal_lod=2.2 dbsnp_normal_lod=5.5