Description

Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through task.ext.args.

Input

name:type
description
pattern

meta

:map

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

assembly

:string

Genome assembly

species

:string

Specie

cache_version

:string

cache version

preflight_check

:boolean

Whether to check that the expected cache file is listed in the Ensembl CHECKSUMS file before downloading

Output

name:type
description
pattern

cache

meta

:file

cache

*

prefix

:file

cache

*

versions_ensemblvep

${task.process}

:string

The process the versions were collected from

ensemblvep

:string

The tool name

vep --help | sed -n '/ensembl-vep/s/.*: //p'

:eval

The command used to generate the version of the tool

versions_perlmathcdf

${task.process}

:string

The process the versions were collected from

perl-math-cdf

:string

The name of the tool

perl -MMath::CDF -e 'print \$Math::CDF::VERSION'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

ensemblvep

:string

The tool name

vep --help | sed -n '/ensembl-vep/s/.*: //p'

:eval

The command used to generate the version of the tool

${task.process}

:string

The process the versions were collected from

perl-math-cdf

:string

The name of the tool

perl -MMath::CDF -e 'print \$Math::CDF::VERSION'

:eval

The expression to obtain the version of the tool

Tools

ensemblvep
Apache-2.0

VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

ensembl.org/info/docs/tools/vep ensembl.org/info/docs/tools/vep/script
included in
pacsomaticrnadnavarrnavarsarektumourevo
maintainer
Github user maxulysse
get in touch
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