The Ensembl Variant Effect Predictor

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

Abstract

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

Keywords: Genome; NGS; SNP; Variant annotation.

Figures

Fig. 1
Fig. 1
A typical VEP Web results page. Section (1) gives summary pie charts and statistics. Section (2) contains a preview of the results table with navigation, filtering, and download options. The preview table contains hyperlinks to genes, transcripts, regulatory features, and variants in the Ensembl browser. The results can be downloaded in VCF, text, or custom VEP file formats
Fig. 2
Fig. 2
Example of JSON output as produced by the VEP script and REST API (redacted and prettified for display)

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