qualimap

The Qualimap module parses results generated by Qualimap, 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:

table_columns_visible:
  QualiMap:
    general_error_rate: True
    median_insert_size: False

See the relevant section of the documentation 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:

qualimap_config:
  general_stats_coverage:
    - 10
    - 20
    - 40
    - 200
    - 30000
  general_stats_coverage_hidden:
    - 10
    - 20
    - 200