vcf2maf-vep

This Dockerfile is loosely based on this gist and can be used to create a Docker image with all of the necessary dependencies for vcf2maf to run with Ensemble v107. You just need to provide (1) the VEP 107 cache (instructions for grabbing it with rsync below) and (2) the genomic FASTA that you aligned to (for the NF-OSI pipeline, we currently use the GATK GRCh38 build, which can be acquired from iGenomes (instructions for grabbing it with the AWS CLI below).

The Docker repository for this is: https://hub.docker.com/r/nfosi/vcf2maf

Currently, this image uses a custom fork of vcf2maf to address a small incompatibility with VEP v107. When mskcc/vcf2maf#322 is resolved, we can switch back to the real release of vcf2maf.

## Need to have rsync and the aws-cliv2 installed.

## Get VEP 107 database. 
rsync -avr --progress rsync://ftp.ensembl.org/ensembl/pub/release-107/variation/indexed_vep_cache/homo_sapiens_vep_107_GRCh38.tar.gz $HOME/.vep/
tar -zxf $HOME/.vep/homo_sapiens_vep_107_GRCh38.tar.gz -C $HOME/.vep/

## Get GATK GRCh38 genome (or whatever genome you aligned to if not this one...)
aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ $HOME/Homo_sapiens_GATK_GRCh38/

## Get vcfs. Place in $HOME/vcfs

gunzip $HOME/vcfs/*

docker run -v $HOME/vcfs:/workdir/vcfs:rw -v $HOME/.vep:/workdir/vep:ro -v $HOME/Homo_sapiens_GATK_GRCh38/Sequence/WholeGenomeFasta:/workdir/fasta:ro -v $HOME/mafs:/workdir/mafs:rw -it --entrypoint /bin/bash nfosi/vcf2maf

cd /nf-osi-vcf2maf-*

##test

perl vcf2maf.pl --input-vcf /workdir/vcfs/28cNF.Strelka.filtered.vcf --output-maf /workdir/test.vep.maf --ref-fasta /workdir/fasta/Homo_sapiens_assembly38.fasta --vep-path /root/miniconda3/envs/vcf2maf/bin --vep-data /workdir/vep --ncbi-build GRCh38

Example loop to run in docker container:

for i in /workdir/vcfs/*.vcf; do
	echo $i 
	ic=$(basename ${i})
    ic=${ic%.Strelka.filtered.vcf}  ##change this to trim to your sample ID as necessary

    echo $ic

    perl vcf2maf.pl --input-vcf $i --output-maf /workdir/${ic}.vep.maf --ref-fasta /workdir/fasta/Homo_sapiens_assembly38.fasta --vep-path /root/miniconda3/envs/vcf2maf/bin --vep-data /workdir/vep --ncbi-build GRCh38 --tumor-id $ic
done

Adding support for --af_gnomadg

Original command

docker run \
	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
	nfosi/vcf2maf:latest \
	perl nf-osi-vcf2maf-1b34293/vcf2maf.pl --input-vcf /work/test-small.vcf \
	--output-maf /work/test-small.maf --vep-data /ref/vep \
	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
	--vep-path /root/miniconda3/envs/vcf2maf/bin --ncbi-build GRCh38

Using vcf2maf.sh

This shell script adds support for --af_gnomadg

docker run \
	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
	-v $HOME/vcf2maf-wf/:/src/:ro \
	nfosi/vcf2maf:latest \
	bash /src/vcf2maf.sh --input-vcf /work/test-small.vcf \
	--output-maf /work/test-small.maf --vep-data /ref/vep \
	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
	--vep-path /root/miniconda3/envs/vcf2maf/bin --ncbi-build GRCh38

Using vcf2maf-gnomad-genomes

This uses a forked version of vcf2maf

docker run \
	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
	sagebionetworks/vcf2maf:gnomad-genomes \
	vcf2maf.pl --input-vcf /work/test-small.vcf \
	--output-maf /work/test-small.maf --vep-data /ref/vep \
	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
	--vep-path /root/miniconda3/envs/vep/bin --ncbi-build GRCh38