ensembl-vep

downloads

The 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.

Home http://www.ensembl.org/info/docs/tools/vep/index.html
Versions 88, 88.10, 88.8, 88.9, 89.1, 89.4, 89.7, 90.1, 90.10, 90.3, 90.5, 90.6, 90.7, 90.9
License Apache 2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/ensembl-vep

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install ensembl-vep

and update with:

conda update ensembl-vep

Notes

This package installs only the variant effect predictor (VEP) library code. To install data libraries, you can use the ‘vep_install’ command installed along with it. For example, to install the VEP library for human GRCh38 to a directory

vep_install -a cf -s homo_sapiens -y GRCh38 -c /output/path/to/GRCh38/vep –CONVERT

(note that vep_install is renamed from INSTALL.pl
to avoid having generic script names in the PATH)

The –CONVERT flag is not required but improves lookup speeds during runs. See the VEP documentation for more details

http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html

docker

A Docker container is available at https://quay.io/repository/biocontainers/ensembl-vep.