Mutect2 PoN allele-specific or less specific position-based?
Can you please confirm that the panel of normals is excluding variants based on chromosome position and not requiring allele-specific matching? ie. a G->A variant in the tumor sample may be filtered if there's a G->T entry at that chromosomal position in the panel of normals. I've seen examples of this and just want to confirm that this is the expected behavior. Thx in advance.
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Hi ,
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Brian Haas Confirmed — it is expected and intended. We would love to do better some day, but for now considering the site bad if there is any artifact is the safest approach.
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