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Are secondary alignments, and duplicates taken into consideration by DepthOfCoverage? How can you skip secondary alignments for coverage estimation?
No, those will not be taken into account by DepthOfCoverage. As indicated in the tech doc, DoC applies several filters by default, including the duplicates filter and the secondary alignments filter. Just check that duplicates have been marked as such in your bam file and you're good to go.