NAME¶

mosdepth - manual page for mosdepth 0.3.6

DESCRIPTION¶

mosdepth 0.3.6

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

Arguments:

<prefix>

outputs: `{prefix}.mosdepth.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:

-t --threads <threads>

number of BAM decompression threads [default: 0]

-c --chrom <chrom>

chromosome to restrict depth calculation.

-b --by <bed|window>

optional BED file or (integer) window-sizes.

-n --no-per-base

dont output per-base depth. skipping this output will speed execution substantially. prefer quantized or thresholded values if possible.

-f --fasta <fasta>

fasta file for use with CRAM files [default: ].

Other options:

-F --flag <FLAG>

exclude reads with any of the bits in FLAG set [default: 1796]

-i --include-flag <FLAG>

only include reads with any of the bits in FLAG set. default is unset. [default: 0]

-x --fast-mode

dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).

-q --quantize <segments>

write quantized output see docs for description.

-Q --mapq <mapq>

mapping quality threshold. reads with a quality less than this value are ignored [default: 0]

-l --min-frag-len <min-frag-len>

minimum insert size. reads with a smaller insert size than this are ignored [default: -1]

-u --max-frag-len <max-frag-len>

maximum insert size. reads with a larger insert size than this are ignored. [default: -1]

-T --thresholds <thresholds>

for each interval in --by, write number of bases covered by at least threshold bases. Specify multiple integer values separated by ','.

-m --use-median

output median of each region (in --by) instead of mean.

-R --read-groups <string>

only calculate depth for these comma-separated read groups IDs.

-h --help

show help