Default autosomal coverage and renamed output for mt pipeline #6160
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Kristen requested some small changes for the mitochondria pipeline. This renames the output vcf with the name of the sample and puts a default value for autosomal_median_coverage (meaning you'll now get the NuMT filter even if you don't provide the actual autosomal coverage). Happy to discuss if that's the right thing to do or if we really want to force people to put a value for autosomal coverage.