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.
Download the latest stable branch of vcf2maf, and view the detailed usage manual:
curl -LO https://github.com/mskcc/vcf2maf/archive/master.zip; unzip master.zip; cd vcf2maf-master
perl vcf2maf.pl --man
To download properly versioned releases, click here for a list.
If you don't have VEP installed, then follow this gist. VEP is preferred for its large team of active coders, and its CLIA-compliant HGVS formats. After installing VEP, you can test the script like so:
perl vcf2maf.pl --input-vcf data/test.vcf --output-maf data/test.vep.maf
To fill columns 16 and 17 of the output MAF with tumor/normal sample IDs, and to parse out genotypes and allele counts from matched genotype columns in the VCF, use options --tumor-id and --normal-id. Skip option --normal-id if you didn't have a matched normal:
perl vcf2maf.pl --input-vcf data/test.vcf --output-maf data/test.vep.maf --tumor-id WD1309 --normal-id NB1308
VCFs from variant callers like VarScan use hardcoded sample IDs TUMOR/NORMAL in the genotype columns of the VCF. To have this script correctly parse the correct genotype columns, while still printing the proper IDs in the output MAF:
perl vcf2maf.pl --input-vcf data/test_varscan.vcf --output-maf data/test_varscan.vep.maf --tumor-id WD1309 --normal-id NB1308 --vcf-tumor-id TUMOR --vcf-normal-id NORMAL
If you have the VEP script in a different folder like /opt/vep, and its cache in /srv/vep, there are options available to use those instead:
perl vcf2maf.pl --input-vcf data/test.vcf --output-maf data/test.vep.maf --vep-path /opt/vep --vep-data /srv/vep
If you have a MAF or a MAF-like file that you want to reannotate, then use maf2maf, which simply runs maf2vcf followed by vcf2maf:
perl maf2maf.pl --input-maf data/test.maf --output-maf data/test.vep.maf
After tests on variant lists from many sources, maf2vcf and maf2maf are quite good at dealing with formatting errors or "MAF-like" files. The bare minimum columns that it expects as input are:
Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Tumor_Sample_Barcode
1 3599659 C T TCGA-A1-A0SF-01
1 6676836 A C TCGA-A1-A0SF-01
1 7886690 G A TCGA-A1-A0SI-01
See data/minimalist_test_maf.tsv for a sampler. Addition of Tumor_Seq_Allele1 will be used to determine zygosity. Otherwise, it will try to determine zygosity from variant allele fractions, assuming that arguments --tum-vad-col and --tum-depth-col are set correctly to the names of columns containing those read counts. Specifying the Matched_Norm_Sample_Barcode with its respective columns containing read-counts, is also strongly recommended.
Apache-2.0 | Apache License, Version 2.0 | https://www.apache.org/licenses/LICENSE-2.0