VEP protocols

VEP specifications

Information


Unique identifier OMICS_00139
Name VEP
Alternative name Variant Effect Predictor
Interface Web user interface, Application programming interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline William McLaren <>

Additional information


http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

Information


Unique identifier OMICS_00139
Name VEP
Alternative name Variant Effect Predictor
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format VCF, variant identifiers and HGVS notations.
Output data Summary file and a primary results file in tab-delimited.
Output format HTML or text format and VCF, GVF, or JSON format.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 88.8
Stability Stable

Taxon


  • Primates
    • Homo sapiens

Download


Versioning


Add your version

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

Publications for Variant Effect Predictor

VEP IN pipelines

 (34)
2018
PMCID: 5761188
PMID: 29316957
DOI: 10.1186/s13058-017-0929-z

[…] [23] and platypus [24] were used for variant calling. annotation of variants was performed using a local copy of the ensembl [25] version r73 database and a customised version of ensembl variant effect predictor. variants were determined by reference to the canonical transcripts. the ensembl definition was as follows: (1) longest consensus coding sequence project translation […]

2018
PMCID: 5804026
PMID: 29391395
DOI: 10.1038/s41398-017-0079-1

[…] of the prs on risk was adjusted for age, sex, chip and pcs 1–8., snps associated (at genome-wide significance) with risk-taking behaviour were further investigated for influence on nearby genes (variant effect predictor, vep20) and for reported associations with relevant traits (gwas catalogue21). descriptions and known or predicted functions of implicated genes were compiled (genecards […]

2018
PMCID: 5804026
PMID: 29391395
DOI: 10.1038/s41398-017-0079-1

[…] adjusted for age, sex, chip and pcs 1–8., snps associated (at genome-wide significance) with risk-taking behaviour were further investigated for influence on nearby genes (variant effect predictor, vep20) and for reported associations with relevant traits (gwas catalogue21). descriptions and known or predicted functions of implicated genes were compiled (genecards www.genecards.org and entrez […]

2018
PMCID: 5884486
PMID: 29617380
DOI: 10.1371/journal.pone.0193515

[…] enhanced the understanding of the relations between snps, genes and pathways., regarding the snps the following database and analyses were performed:, 1) snp descriptions were obtained from ensembl vep, in which we checked the variant location and the consequences of the variation on the dna sequence (i.e. intronic, missense, regulatory, etc)., 2) ensembl variation database was consulted […]

2018
PMCID: 5940669
PMID: 29740198
DOI: 10.1038/s41598-018-25669-1

[…] indels was set to 0.05 instead of 0.15; complex variant detection was enabled). called variants were annotated using a custom pipeline based on vcflib (https://github.com/ekg/vcflib), snpsift37, the variant effect predictor (vep) software38 and ncbi refseq database. confident somatic mutations were obtained from annotated variants by: i) filtering-out germline mutations identified in matched […]

VEP institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
VEP funding source(s)
Supported by the Wellcome Trust (grant numbers WT095908 and WT098051), the European Molecular Biology Laboratory, the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 (GEN2PHEN) and under grant agreement number 222664 (Quantomics) and from the European Union’s Horizon 2020 research and innovation programme under grant agreement number 634143 (MedBioinformatics).

VEP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review VEP