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DepthOfCoverage missing to report some locations
Dear GATK team
We recently noticed that some DepthOfCoverage output (no suffix: per locus coverage) is missing to report some locations of the BED file input. This was a bit more odd when the same locations were actually reported for a different base-quality cut-off.
Specifically, there are locations of the BED file that have output entries for -mbq 30 but don't for -mbq 20.
Irrespective of -mbq, from what it's read from the documentation (no suffix: per locus coverage) I would assume that the output contain all locations of the BED reported even if the coverage is zero. Right?
Would you please clarify how the actual engine works?