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Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial
Author(s) -
Hunt Sarah E.,
Moore Benjamin,
Amode Ridwan M.,
Armean Irina M.,
Lemos Diana,
Mushtaq Aleena,
Parton Andrew,
Schuilenburg Helen,
Szpak Michał,
Thormann Anja,
Perry Emily,
Trevanion Stephen J.,
Flicek Paul,
Yates Andrew D.,
Cunningham Fiona
Publication year - 2022
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.24298
Subject(s) - ensembl , computer science , annotation , refseq , exposome , gene annotation , interface (matter) , computational biology , bioinformatics , biology , genomics , genome , genetics , artificial intelligence , gene , operating system , bubble , maximum bubble pressure method
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 consequences 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 Sorting Intolerant From Tolerant and Combined Annotation Dependent Depletion. Ensembl VEP includes filtering options to customize variant prioritization. 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 application programming interface, 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, visualization, 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.