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mutect2 filter fieild


We found a mutation was tagged as "PASS" in FILTER field with mutect2 (3.6 version) for some samples, however, this mutation is in our Panel of normal. For some other samples, this mutation was tagged as "panel_of_normals" correctly with the same version of mutect2. How can we explain why a PON mutation was tagged as "PASS" sometimes?

Let me know if you need any details information.



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Rebecca,

    It is possible for a variant to PASS even when the variant is in the PON. MuTect2 simply applies a higher threshold to pass when the variant is in the PON. In your case, the PASS variant would have been higher than the threshold, so it did not fail the filters.


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