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

]

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 (file)

annotated vcf (optional)

*.ann.vcf.gz

tab (file)

tab file with annotated variants (optional)

*.ann.tab.gz

json (file)

json file with annotated variants (optional)

*.ann.json.gz

report (file)

VEP report file

*.html

versions (file)

File containing software versions

versions.yml
included in
raredisease rnadnavar sarek variantcatalogue
maintainers
Github user maxulysse
Github user matthdsm
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

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