MOSDEPTH(1)

✨ NAME ✨

mosdepth — the manual page for mosdepth 0.3.11, bestie 💖 (you'll also see it filed under MOSDEPTH(1))

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🌸 DESCRIPTION 🌸

okay so, we're on mosdepth 0.3.11 and here's literally how you run it:

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

that's the whole vibe. two positional things, a pile of options, and a bunch of very cute output files. let's get into it 🫶

🎀 Arguments 🎀

• <prefix> — this is your output name stem, and the way it's giving main character energy... every single file below gets built off it:
  • {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. yes, exactly that. hand it over 🔥

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🧚 Common Options 🧚

• -t, --threads <threads> — number of BAM decompression threads [default: 0]
• -c, --chrom <chrom> — restrict the depth calculation to this one chromosome. just the one, we're being picky 💅
• -b, --by <bed|window> — optional BED file, or an (integer) window-sizes. your call bestie
• -n, --no-per-base — dont output per-base depth. skipping this output will speed execution substantially. prefer quantized or thresholded values if possible.

ngl, if you can live without per-base, do it — it's the single biggest speed glow-up on this list ✨

• -f, --fasta <fasta> — fasta file for use with CRAM files [default: ]. CRAM girlies, this one's for you 🧬

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👑 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). lowkey the default move for most people, fr fr
• -a, --fragment-mode — count the coverage of the full fragment including the full insert (proper pairs only). full send, not just the read 🫶
• -q, --quantize <segments> — write quantized output see docs for description. iykyk
• -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 ,. yes, comma-separated, no spaces, we don't make the rules 💀
• -m, --use-median — output median of each region (in --by) instead of mean. median supremacy 🎀
• -R, --read-groups <string> — only calculate depth for these comma-separated read groups IDs.
• -h, --help — show help. the classic. the icon. when in doubt, hit it 🌈

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heads up bestie: --by is doing a lot of heavy lifting here — regions.bed.gz, thresholds.bed.gz and use-median all hinge on it, so if something's not showing up, check whether you actually passed --by 🦋

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and that's the whole page!! this was mosdepth 0.3.11, dated September 2025, living in section MOSDEPTH(1) of your friendly neighbourhood manual 🌸 go calculate some depth, you've got this, mwah 💅💖