mosdepth - manual page for mosdepth 0.3.3
mosdepth 0.3.3
- 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]
- -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