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Mutect2 output filtering for germline and somatic variants

AKWAKW LuxembourgMember


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?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Anke,

    Basically, PASS variants are high confidence somatic variants. The failing variants (anything other than PASS in filter field) are emitted because they passed quality thresholds, but are not high confidence. So, instead of having to do filtering yourself on a raw VCF, MuTect2 does the filtering for you.

    You can read more about the filters in the VCF header. Also, have a look at the MuTect2 presentation here.


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