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.
|Versions||83, 86, 87|
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
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
A Docker container is available at https://quay.io/repository/biocontainers/variant-effect-predictor.