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Migrate preprocessing stages out of ADAM #598
I vote for avocado, but I'm fine with either one.
(Note, in the branch in avocado I have for mutect, I've also included other pre-processing steps. It's convenient, and it'd be nice if avocado included "necessary pre-processing steps" too.)
I think the only exception to this might be the mark duplicates implementation -- I believe that that's a pre-processing step for some ChIP-seq (i.e. non-variant-calling) pipelines too.