Description

vcf2maf

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

vcf:file

vcf to convert to MAF format. Must be uncompressed.

fasta:file

Path to reference genome fasta file.

vep_cache:file

Path to VEP cache dir. Required for correct running of VEP.

Output

name:type
description
pattern

maf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.maf:file

MAF file produced from VCF

*.maf

versions

versions.yml:file

File containing software versions

versions.yml

Tools

vcf2maf
Apache-2.0

"Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF."

github.com/mskcc/vcf2maf 10.5281/zenodo.593251
included in
tumourevo
maintainer
Github user adamrtalbot
get in touch
Ask a question on Slack Open an issue on GitHub