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gatk 4.05 and "fix_misencoded_quality_scores"
Switching from gatk 3.8 to 4.05 to avail myself of '--enotype-filtered-alleles' I discovered a few format changes to familiar options.
But '--fix_misencoded_quality_scores' is no longer recognized.
My question is what does HC (gatk 4) do when it encounters the problems that were previously handled with the '--fix_misencoded_quality_scores' option?