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mosdepth

manual page for mosdepth 0.3.11

mosdepth 0.3.11

Usage: mosdepth [options] <prefix> <BAM-or-CRAM>

Arguments:

<prefix>
outputs: `{prefix}.mosdepth.global.dist.txt`
`{prefix}.mosdepth.summary.txt`
`{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified) `{prefix}.regions.bed.gz` (if --by is specified) `{prefix}.quantized.bed.gz` (if --quantize is specified) `{prefix}.thresholds.bed.gz` (if --thresholds is specified)
<BAM-or-CRAM>
the alignment file for which to calculate depth.

Common Options:

number of BAM decompression threads [default: 0]
chromosome to restrict depth calculation.
optional BED file or (integer) window-sizes.
dont output per-base depth. skipping this output will speed execution substantially. prefer quantized or thresholded values if possible.
fasta file for use with CRAM files [default: ].

Other options:

exclude reads with any of the bits in FLAG set [default: 1796]
only include reads with any of the bits in FLAG set. default is unset. [default: 0]
dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).
count the coverage of the full fragment including the full insert (proper pairs only).
write quantized output see docs for description.
mapping quality threshold. reads with a quality less than this value are ignored [default: 0]
minimum insert size. reads with a smaller insert size than this are ignored [default: -1]
maximum insert size. reads with a larger insert size than this are ignored. [default: -1]
for each interval in --by, write number of bases covered by at least threshold bases. Specify multiple integer values separated by ','.
output median of each region (in --by) instead of mean.
only calculate depth for these comma-separated read groups IDs.
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