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DepthOfCoverage missing to report some locations

aminziaaminzia aminziaMember

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?

Thank you
Regards
Amin Zia

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