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Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial
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, al...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613081/ https://www.ncbi.nlm.nih.gov/pubmed/34816521 http://dx.doi.org/10.1002/humu.24298 |
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author | 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 |
author_facet | 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 |
author_sort | Hunt, Sarah E. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7613081 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
record_format | MEDLINE/PubMed |
spelling | pubmed-76130812022-08-01 Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial 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 Hum Mutat Article 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. 2022-08 2021-12-02 /pmc/articles/PMC7613081/ /pubmed/34816521 http://dx.doi.org/10.1002/humu.24298 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) International license. |
spellingShingle | Article 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 Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title | Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title_full | Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title_fullStr | Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title_full_unstemmed | Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title_short | Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial |
title_sort | annotating and prioritizing genomic variants using the ensembl variant effect predictor—a tutorial |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7613081/ https://www.ncbi.nlm.nih.gov/pubmed/34816521 http://dx.doi.org/10.1002/humu.24298 |
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