What is the best way to map Mutect2 input command-line arguments and output VCF fields to the variables described in the Mutect2 whitepaper in its GitHub repo? It isn't obvious to me which variables in the algorithm descriptions there correspond to which fields in the inputs and outputs. Also, is that whitepaper the latest and greatest description of Mutect2 theory? I see it hasn't been updated in 10 months on the master branch. If not, where should I be looking for this info?
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