variant-effect-predictor

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 83, 86, 87
License Apache 2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/variant-effect-predictor

Installation

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

conda install variant-effect-predictor

and update with:

conda update variant-effect-predictor

Notes

This package installs only the variant effect predictor (VEP) library code. To install data libraries, you can use the ‘vep_install.pl’ command installed along with it. For example, to install the VEP library for human hg19/GRCh37 to a directory

vep_install.pl -a cf -s homo_sapiens -y GRCh37 -c /output/path/to/hg19/vep vep_convert_cache.pl -species homo_sapiens -version 86_GRCh37 -d /output/path/to/hg19/vep

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

The convert cache step is not required but improves lookup speeds during runs. See the VEP documentation for more details

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

docker

A Docker container is available at https://quay.io/repository/biocontainers/variant-effect-predictor.