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.

• vcf2maf Main Site: vcf2maf on GitHub
• Type vcf2maf.pl --man to see a brief summary of the options

• Module Name: vcf2maf (see the modules page for more information)
• Multithreaded
• Environment variables set
  • VCF2MAF_HOME
• Example files in $VCF2MAF_HOME/tests
• Reference data in /fdb/VEP/*/cache -- depends on version of VEP loaded
• vcf2maf.pl depends heavily on VEP. At present, only versions of VEP < 107 are compatible.
• Typically vcf2maf.pl requires at least 20g of memory and minimally 4 cpus.
• While VEP is tolerant of chromosome format mismatches (when the input .vcf file uses the UCSC format chrN and the reference fasta uses Ensembl/NCBI format N), vcf2maf is not. Make sure the reference fasta chromosome format matches that of your input.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load VEP/106 vcf2maf

[user@cn3144 ~]$ rm -rf test_{vcf2maf,maf2maf,maf2vcf}
[user@cn3144 ~]$ mkdir test_vcf2maf && cd $_
[user@cn3144 ~]$ cp  $VCF2MAF_EXAMPLES/test.vcf .
[user@cn3144 ~]$ vcf2maf.pl \
  --input-vcf test.vcf \
  --output-maf test.maf \
  --vep-path $VEP_HOME/bin \
  --vep-data $VEP_CACHEDIR \
  --ref-fasta $VEP_CACHEDIR/GRCh38.fa \
  --ncbi-build GRCh38 \
  --cache-version $VEP_VERSION \
  --vep-forks ${SLURM_CPUS_ON_NODE:-2} \
  --verbose
[user@cn3144 ~]$ cd ..

[user@cn3144 ~]$ mkdir test_maf2maf && cd $_
[user@cn3144 ~]$ cp $VCF2MAF_EXAMPLES/test.maf .
[user@cn3144 ~]$ maf2maf.pl \
  --input-maf test.maf \
  --output-maf test.vep.maf \
  --ref-fasta $VEP_CACHEDIR/GRCh37.fa \
  --vep-path $VEP_HOME/bin \
  --vep-data $VEP_CACHEDIR
[user@cn3144 ~]$ cd ..

[user@cn3144 ~]$ mkdir test_maf2vcf && cd $_
[user@cn3144 ~]$ cp $VCF2MAF_EXAMPLES/test.maf .
[user@cn3144 ~]$ maf2vcf.pl \
  --input-maf test.maf \
  --output-dir vcfs \
  --ref-fasta $VEP_CACHEDIR/GRCh37.fa

Create a batch input file (e.g. vcf2maf.sh). For example:

#!/bin/bash
module load VEP/106 vcf2maf
vcf2maf.pl --input-vcf /path/to/data/test.vcf --output-maf test.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION \
  --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] vcf2maf.sh

Create a swarmfile (e.g. vcf2maf.swarm). For example:

vcf2maf.pl --input-vcf data/test1.vcf --output-maf data/test1.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE
vcf2maf.pl --input-vcf data/test2.vcf --output-maf data/test2.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE
vcf2maf.pl --input-vcf data/test3.vcf --output-maf data/test3.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE
vcf2maf.pl --input-vcf data/test4.vcf --output-maf data/test4.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE

Submit this job using the swarm command.

swarm -f vcf2maf.swarm [-g #] [-t #] --module vcf2maf VEP/106