Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.
disable NotPrimaryAlignmentFilter in DepthOfCoverage
Can someone point me to documentation on how I can run DepthOfCoverage without the NotPrimaryAlignmentFilter?
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