The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?