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

cache:file

path to VEP cache (optional)

meta2: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

*.vcf.gz:file

annotated vcf (optional)

*.vcf.gz

tbi

meta:map

Map with sample information

*.vcf.gz.tbi:file

annotated vcf index (optional)

*.vcf.gz.tbi

tab

meta:file

tab file with annotated variants (optional)

*.ann.tab.gz

*.tab.gz:file

tab file with annotated variants (optional)

*.ann.tab.gz

json

meta:file

json file with annotated variants (optional)

*.ann.json.gz

*.json.gz:file

json file with annotated variants (optional)

*.ann.json.gz

report

*.html:file

VEP report file

*.html

versions

versions.yml:file

File containing software versions

versions.yml

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
raredisease rnadnavar rnavar sarek tumourevo variantcatalogue
Github user maxulysse
Github user matthdsm
Github user nvnieuwk
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