---
title: "convert_vcfs_to_maf"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{convert_vcfs_to_maf}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```


```{r setup}
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):
  a) Single Tumour VCF with 2 'sample' columns (one for TUMOR and one for GERMLINE)
  b) Single Tumour VCF with no 'sample' columns (assume all mutations are somatic / Unknown)
2. VEP-annotate your VCF (preferably VEP100, for consistency with the main packages)
3. Convert to MAF with vcf2maf(`path_to_vcf`)