convert_vcfs_to_maf

library(vcf2mafR)

Rationale

This vignette describes the workflow of converting a VCF file to a MAF file.

There are 3 steps:

  1. Ensure you VCF file has a valid structure (we should autodetect):
  1. Single Tumour VCF with 2 ‘sample’ columns (one for TUMOR and one for GERMLINE)
  2. Single Tumour VCF with no ‘sample’ columns (assume all mutations are somatic / Unknown)
  1. VEP-annotate your VCF (preferably VEP100, for consistency with the main packages)
  2. Convert to MAF with vcf2maf(path_to_vcf)