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Variant Effect Predictor VEP script


Quick start
  1. Download latest version (76)
  2. Unpack
    unzip ensembl-tools-release-76.zip
  3. Install
    cd ensembl-tools-release-76/scripts/variant_effect_predictor/
    perl INSTALL.pl
  4. Test
    perl variant_effect_predictor.pl -i example.vcf --cache

Use the VEP script to analyse your variation data locally. No limits, powerful, fast and extendable, the VEP script is the best way to get the most out of the VEP and Ensembl.

The VEP is a powerful and highly configurable tool - have a browse through the documentation. You might also like to read up on the data formats that the VEP uses, and the different ways you can access genome data. The VEP script can annotate your variants with custom data, be extended with plugins, and use powerful filtering to find biologically interesting results.

Beginners should have a run through the tutorial, or try the web interface first.

If you use the VEP in your work, please cite McLaren et. al. (doi:10.1093/bioinformatics/btq330)

Any questions? Send an email to the Ensembl developers' mailing list or contact the Ensembl Helpdesk.