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
|
---
name: Qualimap
url: http://qualimap.bioinfo.cipf.es/
description: >
Qualimap is a platform-independent application to facilitate the quality
control of alignment sequencing data and its derivatives like feature
counts.
---
The Qualimap module parses results generated by
[Qualimap](http://qualimap.bioinfo.cipf.es/),
a platform-independent application to facilitate the quality
control of alignment sequencing data and its derivatives like feature
counts.
The MultiQC module supports the Qualimap commands `BamQC` and `RNASeq`.
Note that Qualimap must be run with the `-outdir` option as well as
`-outformat HTML` (which is on by default). MultiQC uses files
found within the `raw_data_qualimapReport` folder (as well as `genome_results.txt`).
Qualimap adds lots of columns to the General Statistics table. To avoid making the table
too wide and bloated, some of these are hidden by default (`Error Rate`, `M Aligned`, `M Total reads`).
You can override these defaults in your MultiQC config file - for example, to show
`Error Rate` by default and hide `Ins. size` by default, add the following:
```yaml
table_columns_visible:
QualiMap:
general_error_rate: True
median_insert_size: False
```
See the [relevant section of the documentation](http://multiqc.info/docs/#hiding-columns) for more detail.
In addition to this, it's possible to customise which coverage thresholds calculated
by the Qualimap BamQC module _(default: 1, 5, 10, 30, 50)_ and which of these are hidden in the
General Statistics tablewhen the report loads _(default: all hidden except 30X)_.
To do this, add something like the following to your MultiQC config file:
```yaml
qualimap_config:
general_stats_coverage:
- 10
- 20
- 40
- 200
- 30000
general_stats_coverage_hidden:
- 10
- 20
- 200
```
|
