I have noted that, as designed for somatic variants caller, MuTect2 includes some logic to skip variant sites that are very clearly germline based on the evidence present in the Normal sample compared to the Tumor sample, for avoiding spending computational resources on germline events.
And it is NOT capable of emitting records for variant calls that are clearly germline unless it is run in artifact-detection mode, which is used for Panel-Of-Normals(PoN) creation.
So, here is my question:
- Could I call germline variants just using Mutect with single tumor mode? (just like the way we create the PoN)
- Could I use the PoN as the germline variants?
Have a good day!