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.
Mutect2 output filtering for germline and somatic variants
I saw already several threads on Mutect2 outputs, but nothing really answered my question. In principle very simple: I am running currently MuTect2 with just one sample (cancer vs normal), I do not have any panel of normals, as I simply do not have them :-).
My question, in order to separate afterwards the somatic variants and the germline variants:
Am I on the safe side to say:
Germline --> Filter: germline_risk
Somatic --> Filter: PASS
Is there other "filter information" I need to keep? What about "alt_allele_in_normal"?
...and, is there anywhere a more detailed description of these filters?