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mosdepth

Mosdepth performs fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

It can generate several output files all with a common prefix and different endings:

  • per-base depth ({prefix}.per-base.bed.gz),
  • mean per-window depth given a window size ({prefix}.regions.bed.gz, if a BED file provided with --by),
  • mean per-region given a BED file of regions ({prefix}.regions.bed.gz, if a window size provided with --by),
  • a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide ({prefix}.mosdepth.global.dist.txt and {prefix}.mosdepth.region.dist.txt),
  • quantized output that merges adjacent bases as long as they fall in the same coverage bins ({prefix}.quantized.bed.gz),
  • threshold output to indicate how many bases in each region are covered at the given thresholds ({prefix}.thresholds.bed.gz)
  • summary output providing region length, coverage mean, min, and max for each region. ({prefix}.mosdepth.summary.txt)

The MultiQC module plots coverage distributions from 2 kinds of outputs:

  • {prefix}.mosdepth.region.dist.txt
  • {prefix}.mosdepth.global.dist.txt

Using "region" if exists, otherwise "global". Plotting 3 figures:

  • Proportion of bases in the reference genome with, at least, a given depth of coverage (cumulative coverage distribution).
  • Proportion of bases in the reference genome with a given depth of coverage (absolute coverage distribution).
  • Average coverage per contig/chromosome.

Also plotting the percentage of the genome covered at a threshold in the General Stats section. The default thresholds are 1, 5, 10, 30, 50, which can be customised in the config as follows:

mosdepth_config:
  general_stats_coverage:
    - 10
    - 20
    - 40
    - 200
    - 30000

You can also specify which columns would be hidden when the report loads (by default, all values are hidden except 30X):

general_stats_coverage_hidden:
  - 10
  - 20
  - 200

For the per-contig coverage plot, you can include and exclude contigs based on name or pattern.

For example, you could add the following to your MultiQC config file:

mosdepth_config:
  include_contigs:
    - "chr*"
  exclude_contigs:
    - "*_alt"
    - "*_decoy"
    - "*_random"
    - "chrUn*"
    - "HLA*"
    - "chrM"
    - "chrEBV"

Note that exclusion superseeds inclusion for the contig filters.

To additionally avoid cluttering the plot, mosdepth can exclude contigs with a low relative coverage.

mosdepth_config:
  # Should be a fraction, e.g. 0.001 (exclude contigs with 0.1% coverage of sum of
  # coverages across all contigs)
  perchrom_fraction_cutoff: 0.001

If you want to see what is being excluded, you can set show_excluded_debug_logs to True:

mosdepth_config:
  show_excluded_debug_logs: True

This will then print a debug log message (use multiqc -v) for each excluded contig. This is disabled by default as there can be very many in some cases.

Besides the {prefix}.mosdepth.global.dist.txt and {prefix}.mosdepth.region.dist.txt files, the {prefix}.mosdepth.summary.txt file is used for the General Stats table.

The module also plots an X/Y relative chromosome coverage per sample. By default, it finds chromosome named X/Y or chrX/chrY, but that can be customised:

mosdepth_config:
  # Name of the X and Y chromosomes. If not specified, MultiQC will search for
  # any chromosome names that look like x, y, chrx or chry (case-insensitive)
  xchr: myXchr
  ychr: myYchr