NAME

       mosdepth - manual page for mosdepth 0.3.11

DESCRIPTION

       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:

       -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).

       -a --fragment-mode
              count the coverage of the full fragment including the full insert (proper pairs only).

       -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

mosdepth 0.3.11                                  September 2025                                      MOSDEPTH(1)