---
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
```
