NAME

       mosdepth - manual page for mosdepth 0.3.3

DESCRIPTION

       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