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Option to emit (but still filter) all germline sites in Mutect2 #4522
@@ Coverage Diff @@ ## master #4522 +/- ## =============================================== - Coverage 79.118% 79.111% -0.007% Complexity 16675 16675 =============================================== Files 1051 1051 Lines 60282 60285 +3 Branches 9874 9875 +1 =============================================== - Hits 47694 47692 -2 - Misses 8764 8765 +1 - Partials 3824 3828 +4
Mar 13, 2018
Thanks for the clarification. To paraphrase the following:
We now have a parameter that allows inclusion of sites that are variant in the tumor that are also variant in the matched-normal and/or present in the germline resource. With the option enabled, these sites are emitted for the tumor and if the matched-normal is part of the analysis, then its variants for the sites are also noted in the callset. Finally, this parameter is set to true with
That's right, and just because more explicitness never hurts, here's another paraphrase.
M2 default: call somatic variation in the tumor sample. Some possible germline variants will be included, but not intentionally.
New option: call all variation in the tumor sample.
In both case FilterMutectCalls is the same. It uses the INFO fields from Mutect2 to put the