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Ensembl VEP determines the effect of your variants on genes, transcripts and protein sequences, as well as regulatory regions.


The VEP module parses the summary statistics generated by Ensembl VEP.

MultiQC parses the 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

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