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?