vcf2mafR

vcf2mafR converts vcf files and vcf-like dataframes to MAF files

This is an unofficial R implementation of VCF to MAF mapping, and is inspired by the official perl implementation: vcf2maf.

vcf2mafR implements only a subset of the functionality available in vcf2maf, so we recommend any users who don’t require a native R solution to use the original!

Installation

You can install the development version of vcf2mafR like so:

# install.packages('remotes')
remotes::install_github('CCICB/vcf2mafR')

Conversions

• df2maf : Converts VCF-like data.frames to MAF format
• vcf2maf: Converts VCF files to MAF format
• vcf2df: Converts VCF files to data.frame formats compatible wth MAF conversion

Quick Start

library(vcf2mafR)

path_vcf_vepped <- system.file("testfiles/test_b38.vepgui.vcf", package = "vcf2mafR")
df <- vcf2df(vcf = path_vcf_vepped)
#> 
#> ── Reading VCF ─────────────────────────────────────────────────────────────────
#> ✔ VCF successfully read
#> 
#> ── Checking VCF is VEP-annotated ───────────────────────────────────────────────
#> ℹ Looking for ##VEP entry in VCF header
#> ✔ Looking for ##VEP entry in VCF header [11ms]
#> 
#> ℹ Checking at least some of our entries have CSQ field in INFO column
#> 
#> ℹ Checking at least some of our entries have CSQ field in INFO column── Converting VCF to data.frame ────────────────────────────────────────────────
#> ℹ Checking at least some of our entries have CSQ field in INFO column✔ Checking at least some of our entries have CSQ field in INFO column [43ms]
#> 
#> ℹ Converting to dataframe
#> ✔ vcf2df successful
#> ℹ Converting to dataframe✔ Converting to dataframe [951ms]