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---
Name: mosdepth
URL: https://github.com/brentp/mosdepth
Description: >
Mosdepth performs fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
---
[Mosdepth](https://github.com/brentp/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`)
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:
```yaml
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):
```yaml
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:
```yaml
mosdepth_config:
include_contigs:
- "chr*"
exclude_contigs:
- "*_alt"
- "*_decoy"
- "*_random"
- "chrUn*"
- "HLA*"
- "chrM"
- "chrEBV"
```
Note that exclusion superseeds inclusion for the contig filters.
If you want to see what is being excluded, you can set `show_excluded_debug_logs` to `True`:
```yaml
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.
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