Description

Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.

Input

name:type
description
pattern

meta

:map

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

vcf

:file

vcf to annotate

custom_extra_files

:file

extra sample-specific files to be used with the --custom flag to be configured with ext.args (optional)

genome

:string

which genome to annotate with

species

:string

which species to annotate with

cache_version

:integer

which version of the cache to annotate with

meta2

:map

Groovy Map containing cache information e.g. [ id:‘test’ ]

cache

:file

path to VEP cache (optional)

meta3

:map

Groovy Map containing fasta reference information e.g. [ id:‘test’ ]

fasta

:file

reference FASTA file (optional)

*.{fasta,fa}

extra_files

:file

path to file(s) needed for plugins (optional)

Output

name:type
description
pattern

vcf

meta

:map

Map with sample information

${prefix}.vcf.gz

:file

annotated vcf (optional)

*.vcf.gz

tbi

meta

:map

Map with sample information

${prefix}.vcf.gz.tbi

:file

annotated vcf index (optional)

*.vcf.gz.tbi

tab

meta

:map

Map with sample information

${prefix}.tab.gz

:file

tab file with annotated variants (optional)

*.ann.tab.gz

json

meta

:map

Map with sample information

${prefix}.json.gz

:file

json file with annotated variants (optional)

*.ann.json.gz

report

meta

:map

Map with sample information

${task.process}

:string

The process

ensemblvep

:string

The tool name

*.html

:file

VEP report file

*.html

versions_ensemblvep

${task.process}

:string

The process

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_tabix

${task.process}

:string

The process

tabix

:string

The tool name

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'

:eval

The expression to obtain the version of the tool

versions_perlmathcdf

${task.process}

:string

The process

perl-math-cdf

:string

The tool name

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

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

multiqc_files

meta

:string

Map with sample information

${task.process}

:string

The process

ensemblvep

:string

The tool name

*.html

:file

VEP report file

*.html

versions

${task.process}

:string

The process

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

tabix

:string

The tool name

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'

:eval

The expression to obtain the version of the tool

${task.process}

:string

The process

perl-math-cdf

:string

The tool name

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
pacsomaticrarediseasernadnavarrnavarsarektumourevovariantcatalogue
maintainers
Github user maxulysse
Github user matthdsm
Github user nvnieuwk
get in touch
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