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.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install ensembl-vep
and update with:
conda update ensembl-vep
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
A Docker container is available at https://quay.io/repository/biocontainers/ensembl-vep.