Vcf2maf

Introduction

To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single effect per variant, is often subjective. So this project is an attempt to make the selection criteria smarter, reproducible, and more configurable. And the default criteria must lean towards best practices.

For more information, please check:
Home page: https://github.com/mskcc/vcf2maf

Versions

  • 1.6.21

Commands

  • maf2maf.pl

  • maf2vcf.pl

  • vcf2maf.pl

  • vcf2vcf.pl

Module

You can load the modules by:

module load biocontainers
module load vcf2maf

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

Note

If users need to use vep, please add --vep-path /opt/conda/bin.

To run vcf2maf on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vcf2maf
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers vcf2maf

vcf2maf.pl --vep-path /opt/conda/bin \
    --ref-fasta Homo_sapiens.GRCh37.dna.toplevel.fa.gz \
    --input-vcf tests/test.vcf --output-maf test.vep.maf