1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
|
---
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`)
- 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:
```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.
To additionally avoid cluttering the plot, mosdepth can exclude contigs with a low relative coverage.
```yaml
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`:
```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.
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:
```yaml
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
```
|
