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F.A.Q.

Why doesn't mosdepth allow a base-quality filter.

mosdepth operates on chunks of reads where the chunks are defined by the cigar string. Usually, a read will have a single chunk (given, e.g. 151M cigar). Since mosdepth does not have to look at base-qualities it is much faster. If you need this, you can trim reads prior to aligning or use samtools depth.