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vcf2maf

repository·main·Indexed 19 days ago

https://github.com/mskcc/vcf2maf

A toolset for converting VCF files into Mutation Annotation Format (MAF) files, standardizing the selection of a single gene transcript or isoform effect per variant. It utilizes Ensembl's Variant Effect Predictor (VEP) for high-quality annotation. The package includes vcf2maf.pl for VCF to MAF conversion and maf2maf.pl for reannotating existing MAF files.

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What's inside vcf2maf

  1. Install vcf2maf and maf2maf

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    To install the latest release of vcf2maf, download the tarball from GitHub, extract it, and navigate to the directory. You can view the detailed usage manuals for the scripts using the --man flag.

    Note: This repository is in a maintenance-only phase and is scheduled for archive in Dec 2026. Consider switching to mafsmith for future projects.

    export VCF2MAF_URL=`curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d" -f4`
curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-*
perl vcf2maf.pl --man
perl maf2maf.pl --man

  2. Reannotate MAF files using maf2maf.pl

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    The maf2maf.pl script is used to reannotate existing MAF or MAF-like files. It works by internally running maf2vcf followed by vcf2maf.

    Required Input Columns

    The script expects at least the following columns:

    • Chromosome
    • Start_Position
    • Reference_Allele
    • Tumor_Seq_Allele2
    • Tumor_Sample_Barcode

    Zygosity and Read Counts

    • If Tumor_Seq_Allele1 is present, it is used to determine zygosity.
    • If not present, zygosity is determined from variant allele fractions using the --tum-vad-col and --tum-depth-col arguments.
    • For matched normal data, use --nrm-vad-col and --nrm-depth-col along with Matched_Norm_Sample_Barcode.
    perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test.vep.maf

  3. Run vcf2maf using Docker

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    You can run the tools inside a Docker container. First, build the image from the repository source, then run the scripts using docker run.

    # Build the image
git clone git@github.com:mskcc/vcf2maf.git
cd vcf2maf
docker build -t vcf2maf:main .
docker builder prune -f

# Run scripts
docker run --rm vcf2maf:main perl vcf2maf.pl --help
docker run --rm vcf2maf:main perl maf2maf.pl --help

  4. Convert VCF to MAF using vcf2maf.pl

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    The vcf2maf.pl script converts VCF files to MAF format. It relies on Ensembl's VEP (Variant Effect Predictor) for annotation.

    Basic Usage

    To perform a standard conversion: perl vcf2maf.pl --input-vcf <input.vcf> --output-maf <output.maf>

    Handling Sample IDs and Genotypes

    • Use --tumor-id and --normal-id to fill columns 16 and 17 of the output MAF with specific sample IDs and to parse genotypes/allele counts from the VCF.
    • If your VCF uses specific hardcoded names for genotype columns (e.g., TUMOR/NORMAL from VarScan), use --vcf-tumor-id and --vcf-normal-id to map them to your desired output IDs.

    VEP Configuration

    If VEP is installed in non-standard locations, specify the paths:

    • --vep-path: Path to the VEP installation.
    • --vep-data: Path to the VEP cache/data.

    Bypassing VEP

    Use --inhibit-vep to skip VEP and create a minimalist MAF-like file using only data from the input VCF. Warning: This is not recommended unless you are certain of the input VCF's annotation quality, as vcf2maf normally runs VEP with specific parameters to ensure standardization.

    # Basic conversion
perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf

# Conversion with sample IDs
perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --tumor-id WD1309 --normal-id NB1308

# Handling VarScan-style VCFs
perl vcf2maf.pl --input-vcf tests/test_varscan.vcf --output-maf tests/test_varscan.vep.maf --tumor-id WD1309 --normal-id NB1308 --vcf-tumor-id TUMOR --vcf-normal-id NORMAL

# Specifying VEP paths
perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --vep-path /opt/vep --vep-data /srv/vep