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VCFTools

Program to analyse and reporting on VCF files

https://vcftools.github.io

Important General Note​

  • Depending on the size and density of the variant data (vcf), some of the stat files generated by vcftools can be very large. If you find that some of your input files are missing, increase the config.log_filesize_limit so that the large file(s) will not be skipped by MultiQC. Note, however, that this might make MultiQC very slow!

This module parses the outputs from VCFTools' various commands:

Implemented​

  • relatedness2
    • Plots a heatmap of pairwise sample relatedness.
    • Not to be confused with the similarly-named command relatedness
  • TsTv-by-count
    • Plots the transition to transversion ratio as a function of alternative allele count (using only bi-allelic SNPs).
  • TsTv-by-qual
    • Plots the transition to transversion ratio as a function of SNP quality threshold (using only bi-allelic SNPs).
  • TsTv-summary
    • Plots a bargraph of the summary counts of each type of transition and transversion SNPs.

To do​

VCFTools has a number of outputs not yet supported in MultiQC which would be good to add. Please check GitHub if you'd like these added or (better still), would like to contribute!

File search patterns​

vcftools/relatedness2:
  fn: "*.relatedness2"
vcftools/tstv_by_count:
  fn: "*.TsTv.count"
vcftools/tstv_by_qual:
  fn: "*.TsTv.qual"
vcftools/tstv_summary:
  fn: "*.TsTv.summary"