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VEP

Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions

https://www.ensembl.org/info/docs/tools/vep/index.html

MultiQC parses the Ensembl VEP summary statistics stored in either HTML or plain text format.

Beside VEP's default naming convention, you can run VEP with one of the options below to use this module:

  • --stats_file [OUTPUT_FILENAME]_summary.html (VEP's default naming convention)
  • --stats_file [SAMPLE_NAME].vep.html (without the vep or summary suffix, MultiQC will ignore the HTML files)
  • --stats_file [SAMPLE_NAME]_vep.html
  • --stats_text --stats_file [SAMPLE_NAME].vep.txt
  • --stats_text --stats_file [SAMPLE_NAME]_vep.txt

See the VEP documentation for more information.

File search patterns​

vep/vep_html:
  contents: VEP summary
  fn: "*.html"
  max_filesize: 1000000
  num_lines: 10
vep/vep_txt:
  contents: "[VEP run statistics]"
  max_filesize: 100000
  num_lines: 1