recipe ensembl-vep

Ensembl Variant Effect Predictor

Homepage

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

License

Apache-2.0

Recipe

/ensembl-vep/meta.yaml

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.

package ensembl-vep

(downloads) docker_ensembl-vep

Versions
101.0-1101.0-0100.4-0100.3-0100.2-0100.1-1100.1-0100.0-099.2-0

101.0-1101.0-0100.4-0100.3-0100.2-0100.1-1100.1-0100.0-099.2-099.1-099.0-098.3-098.2-098.1-098.0-198.0-097.4-097.3-097.2-097.1-097.0-096.3-096.0-095.3-095.2-095.1-095.0-195.0-094.5-094.4-094.0-093.4-093.2-092.4-092.3-092.0-191.3-191.3-091.2-091.1-091.0-090.10-090.9-190.7-190.7-090.6-090.5-090.3-090.1-190.1-089.7-089.4-089.1-289.1-188.10-188.10-088.9-288.9-188.9-088.8-088-0

Depends
Required By

Installation

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

conda install ensembl-vep

and update with:

conda update ensembl-vep

or use the docker container:

docker pull quay.io/biocontainers/ensembl-vep:<tag>

(see ensembl-vep/tags for valid values for <tag>)

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