taf-mosdepth

taf-mosdepth packages mosdepth 0.3.14-r2, a fast depth and coverage calculator for BAM and CRAM alignment files.

Package identity:

• name: mosdepth
• command: taf-mosdepth
• kind: tool
• TAFFISH version: 0.3.14-r2
• container image: ghcr.io/taffish/mosdepth:0.3.14-r2
• upstream release/tag: v0.3.14
• runtime version string: mosdepth 0.3.14
• native container platform: linux/amd64
• upstream license: MIT
• mosdepth SHA256: c5182b74a8f1b66710efa16e122cbc8a197834874b103e7c5c0bd9a6265ae7b6
• mosdepth_d4 SHA256: d94d545aef6490ea91f348bcebb2ed74b3e2d1c635abc10d8a65dc8387606160
• source archive SHA256: abac67de4547dc5642efd46846044d6b3536d2ca3443b4ca172446edf82eeb42

What Is Included

This app installs the official upstream static Linux release binaries:

• mosdepth
• mosdepth_d4, the D4-enabled binary for --d4 output

The image also includes a small upstream test-data subset under /opt/mosdepth/share/testdata for smoke verification. It does not install Samtools, aligners, reference genomes, or plotting dependencies.

Command Mode

taf-mosdepth --help prints this TAFFISH app help. taf-mosdepth -- --help passes --help to the default upstream mosdepth command.

Mosdepth's first required argument is an output prefix, so normal runs should either use -- before upstream arguments or use command mode with the executable name:

taf-mosdepth -- -n sample sample.bam
taf-mosdepth -- --by targets.bed sample sample.bam
taf-mosdepth mosdepth -n sample sample.bam
taf-mosdepth mosdepth_d4 --d4 sample sample.bam

Avoid taf-mosdepth sample sample.bam; with command_mode = true, TAFFISH may treat sample as a container command rather than as the mosdepth output prefix.

Common Workflows

Summary and distribution only:

taf-mosdepth -- -n --fast-mode sample sample.bam

Per-base depth:

taf-mosdepth -- sample sample.bam

Mean depth over BED intervals:

taf-mosdepth -- -n --by targets.bed sample sample.bam

Threshold counts for each interval:

taf-mosdepth -- -n --by targets.bed --thresholds 1,10,20,30 sample sample.bam

Quantized callable-style regions:

MOSDEPTH_Q0=NO_COVERAGE MOSDEPTH_Q1=LOW_COVERAGE MOSDEPTH_Q2=CALLABLE \
  taf-mosdepth -- -n --quantize 0:1:5:150: sample sample.bam

D4 per-base output:

taf-mosdepth mosdepth_d4 --d4 sample sample.bam

CRAM input with a reference FASTA:

taf-mosdepth -- -n --fast-mode -f reference.fa sample sample.cram

Outputs

Depending on options, mosdepth writes:

• <prefix>.mosdepth.global.dist.txt
• <prefix>.mosdepth.summary.txt
• <prefix>.per-base.bed.gz
• <prefix>.regions.bed.gz
• <prefix>.quantized.bed.gz
• <prefix>.thresholds.bed.gz
• D4 output when using mosdepth_d4 --d4

Per-base output can be large. Use -n, --by, --quantize, or --thresholds when summary, regional, callable, or threshold output is sufficient.

Boundaries

This app packages mosdepth itself. It expects users to provide sorted and indexed BAM or CRAM files. It does not create alignments, sort/index BAMs, build reference indexes, or provide reference genomes.

The upstream release binaries are static and have no runtime libhts.so dependency. CRAM decoding still follows normal htslib behavior and may require a matching reference FASTA via -f or site-specific reference configuration.

The packaged upstream binaries are x86-64 only. Docker and Podman runs request --platform linux/amd64 through src/main.taf. On arm64 hosts this is amd64 emulation, not native arm64 support. Apptainer availability depends on the local system's ability to run amd64 images.

Smoke tests cover version/help/static-linkage checks, summary-only output, per-base output, BED interval output, thresholds, quantized labels, the v0.3.14 chrom-end region fix, and mosdepth_d4 --help. They do not run a full D4 write path because D4 output size is data- and reference-dependent, and they do not test remote BAM/CRAM URLs or large production datasets.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream mosdepth software is covered by: MIT. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/brentp/mosdepth
• Upstream release: https://github.com/brentp/mosdepth/releases/tag/v0.3.14
• Upstream documentation: https://github.com/brentp/mosdepth#usage
• Upstream license: MIT

Citation:

• Pedersen BS, Quinlan AR. 2018. mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. DOI: 10.1093/bioinformatics/btx699, PMID: 29096012.