---
name: "mosdepth"
section: "1"
platform: "linux"
package: "mosdepth"
version: "0.3.3+ds-2"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mosdepth"
---

# mosdepth(1)

manual page for mosdepth 0.3.3

## 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