🚨 Users have reported decreased Mutect2 variant calling accuracy in versions 18.104.22.168 and later🚨
We suspect the issue results from an update making Mutect2 more sensitive to particular edge cases, which are not represented in the publicly-distributed PoN generated by an earlier GATK version. We are investigating the issue and will try to solve it by producing a new Panel of Normals file with the newer version. In the mean time we recommend using Mutect2 from GATK 22.214.171.124.
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