Can you please provide
a) GATK version used: 220.127.116.11
b) Exact GATK commands used: None
c) The entire error log if applicable: None
We know that, in previous versions of GATK, like 4.1.2, Mutect2 does not support MNPs, and should add an argument of "--max-mnp-distance 0" to inhibit MNPs.
I noticed that in the relase information of 18.104.22.168, it is announced that MNPs are supported.
Should we remove "--max-mnp-distance 0" in Panel of Normals creating and Mutation Calling?
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