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.
Cosideration of secondary alignments and duplicates in DepthOfCoverage?
Are secondary alignments, and duplicates taken into consideration by DepthOfCoverage? How can you skip secondary alignments for coverage estimation?
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