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Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial
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  • Sarah Hunt,
  • Benjamin Moore,
  • M. Amode,
  • Irina Armean,
  • Diana Lemos,
  • Aleena Mushtaq,
  • Andrew Parton,
  • Helen Schuilenburg,
  • Michał Szpak,
  • Anja Thormann,
  • Emily Perry,
  • Stephen Trevanion,
  • Paul Flicek,
  • Fiona Cunningham,
  • Andrew Yates
Sarah Hunt
European Molecular Biology Laboratory, European Bioinformatics Institute
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Benjamin Moore
European Molecular Biology Laboratory, European Bioinformatics Institute
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M. Amode
European Molecular Biology Laboratory, European Bioinformatics Institute
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Irina Armean
European Molecular Biology Laboratory, European Bioinformatics Institute
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Diana Lemos
European Molecular Biology Laboratory, European Bioinformatics Institute
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Aleena Mushtaq
European Molecular Biology Laboratory, European Bioinformatics Institute
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Andrew Parton
European Molecular Biology Laboratory, European Bioinformatics Institute
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Helen Schuilenburg
European Molecular Biology Laboratory, European Bioinformatics Institute
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Michał Szpak
European Molecular Biology Laboratory, European Bioinformatics Institute
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Anja Thormann
European Molecular Biology Laboratory, European Bioinformatics Institute
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Emily Perry
European Molecular Biology Laboratory, European Bioinformatics Institute
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Stephen Trevanion
European Molecular Biology Laboratory, European Bioinformatics Institute
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Paul Flicek
European Molecular Biology Laboratory, European Bioinformatics Institute
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Fiona Cunningham
European Molecular Biology Laboratory, European Bioinformatics Institute
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Andrew Yates
European Molecular Biology Laboratory, European Bioinformatics Institute
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Abstract

The Ensembl Variant Effect Predictor (VEP) is a freely available, open source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequence using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as SIFT and CADD. Ensembl VEP includes filtering options to customise variant prioritisation. It is well supported and updated roughly quarterly to incorporate the latest gene, variant and phenotype association information. Ensembl VEP analysis can be performed using a highly configurable, extensible command-line tool, a Representational State Transfer (REST) application programming interface (API) and a user-friendly web interface. These access methods are designed to suit different levels of bioinformatics experience and meet different needs in terms of data size, visualisation and flexibility. In this tutorial, we will describe performing variant annotation using the Ensembl VEP web tool, which enables sophisticated analysis through a simple interface.

Peer review status:IN REVISION

03 May 2021Submitted to Human Mutation
04 May 2021Assigned to Editor
04 May 2021Submission Checks Completed
25 Jun 2021Reviewer(s) Assigned
22 Jul 2021Review(s) Completed, Editorial Evaluation Pending
25 Jul 2021Editorial Decision: Revise Minor