Description

vcf2maf

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

vcf to convert to MAF format. Must be uncompressed.

vep_cache (file)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

maf (file)

MAF file produced from VCF

*.maf

versions (file)

File containing software versions

versions.yml
maintainer
Github user adamrtalbot
get in touch
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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