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The Ensembl Variant Effect Predictor

By William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham

Posted 04 Mar 2016
bioRxiv DOI: 10.1101/042374 (published DOI: 10.1186/s13059-016-0974-4)

The Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation and prioritization of genomic variants, including in non-coding regions. The VEP accurately predicts the effects of sequence variants on transcripts, protein products, regulatory regions and binding motifs by leveraging the high quality, broad scope, and integrated nature of the Ensembl databases. In addition, it enables comparison with a large collection of existing publicly available variation data within Ensembl to provide insights into population and ancestral genetics, phenotypes and disease. The VEP is open source and free to use. It is available via a simple web interface (http://www.ensembl.org/vep), a powerful downloadable package, and both Ensembl’s Perl and REST application program interface (API) services.

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