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QualiMap

Quality control of alignment data and its derivatives like feature counts

http://qualimap.bioinfo.cipf.es/

The 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

File search patterns​

qualimap/bamqc/coverage:
  fn: coverage_histogram.txt
qualimap/bamqc/gc_dist:
  fn: mapped_reads_gc-content_distribution.txt
qualimap/bamqc/genome_fraction:
  fn: genome_fraction_coverage.txt
qualimap/bamqc/genome_results:
  fn: genome_results.txt
qualimap/bamqc/insert_size:
  fn: insert_size_histogram.txt
qualimap/rnaseq/coverage:
  fn: coverage_profile_along_genes_(total).txt
qualimap/rnaseq/rnaseq_results:
  fn: rnaseq_qc_results.txt