Stacks

Analyzes restriction enzyme-based data (e.g. RAD-seq)

http://catchenlab.life.illinois.edu/stacks/

This module is designed to only parse some of the output from the Stacks denovo_map pipeline.

The module works with Stacks version 2.1 or greater.

If you are missing some functionality, please submit an issue on the MultiQC github page

File search patterns

stacks/gstacks:
  contents: BEGIN effective_coverages_per_sample
  fn: gstacks.log.distribs
stacks/populations:
  contents: BEGIN missing_samples_per_loc_prefilters
  fn: populations.log.distribs
stacks/sumstats:
  contents: "# Pop ID\tPrivate\tNum_Indv\tVar\tStdErr\tP\tVar"
  fn: "*.sumstats_summary.tsv"
  max_filesize: 1000000