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, see the sections below. VEP is preferred for it's CLIA-compliant HGVS formats, and is used by default. So after installing VEP, you can test the script like so:
perl vcf2maf.pl --input-vcf data/test.vcf --output-maf data/test.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.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.maf --tumor-id WD1309 --normal-id NB1308 --vcf-tumor-id TUMOR --vcf-normal-id NORMAL
If you have VEP in a different folder like /opt/vep, and cached in /srv/vep, there are options available to point the script there:
perl vcf2maf.pl --input-vcf data/test.vcf --output-maf data/test.maf --vep-path /opt/vep --vep-data /srv/vep
If you have 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
Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
sudo yum install -y curl rsync tar make perl perl-core
## OR ##
sudo apt-get install -y curl rsync tar make perl perl-base
Handle VEP's Perl dependencies using cpanminus to install them under ~/perl5:
curl -L http://cpanmin.us | perl - --notest -l ~/perl5 LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes
Set PERL5LIB to find those libraries. Add this to the end of your ~/.bashrc to make it persistent:
export PERL5LIB=~/perl5/lib/perl5:~/perl5/lib/perl5/x86_64-linux
Create temporary shell variables pointing to where we'll store VEP and its cache data (non default paths can be used, but specify --vep-path and --vep-data when running vcf2maf):
export VEP_PATH=~/vep
export VEP_DATA=~/.vep
Download the v81 release of VEP:
mkdir $VEP_PATH $VEP_DATA; cd $VEP_PATH
curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/81.tar.gz
tar -zxf 81.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'
Download and unpack VEP's offline cache for GRCh37, GRCh38, and GRCm38:
rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_81_GRCh{37,38}.tar.gz $VEP_DATA
rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/mus_musculus_vep_81_GRCm38.tar.gz $VEP_DATA
cat $VEP_DATA/*_vep_81_GRC{h37,h38,m38}.tar.gz | tar -izxf - -C $VEP_DATA
Install the Ensembl API and download the reference FASTAs for GRCh37, GRCh38, and GRCm38:
cd $VEP_PATH
perl INSTALL.pl --AUTO afp --SPECIES homo_sapiens,mus_musculus --ASSEMBLY GRCh38,GRCm38 --PLUGINS CADD,ExAC,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
perl INSTALL.pl --AUTO afp --SPECIES homo_sapiens --ASSEMBLY GRCh37 --PLUGINS CADD,ExAC,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
Convert the offline cache for use with tabix, that significantly speeds up the lookup of known variants:
perl convert_cache.pl --species homo_sapiens,mus_musculus --version 81_GRCh37,81_GRCh38,81_GRCm38 --dir $VEP_DATA
Test running VEP in offline mode, on the provided sample GRCh38 VCF:
perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh38 --offline --no_progress --everything --shift_hgvs 1 --check_existing --check_alleles --total_length --allele_number --no_escape --xref_refseq --dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/81_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa --input_file example_GRCh38.vcf --output_file example_GRCh38.vep.txt
Cyriac Kandoth (ckandoth@gmail.com)
Apache-2.0 | Apache License, Version 2.0 | https://www.apache.org/licenses/LICENSE-2.0