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?

NeelamNeelam Posts: 6Member

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

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