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


  • Animals
    • 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


  • Animals
    • 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

VEP articles

VEP citations

 (14)
2018
PMCID: 5940669

[…] 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 […]

2018
PMCID: 5761188

[…] [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 […]

2017
PMCID: 5736598

[…] developed specifically to detect disease causing variants in sequenced pedigrees32,33. the presence of the hoxb13 g84e variant was examined in the annotated variant list generated using the ensembl variant effect predictor and overlapped with ensembl canonical transcripts., sanger sequencing was performed to validate the wgs results in the original pctas72 carriers, as well as determine […]

2017
PMCID: 5731188

[…] predict functional consequences of candidate variants in conjunction with the ensembl umd3.1.82 gene annotations. variants predicted to impact protein-coding sequences were also annotated using the variant effect predictor [20] (ensembl release 87). for eqtl analyses, transformed gene expression phenotypes for all expressed genes overlapping each of the 1mbp windows were used to identify eqtl, […]

2016
PMCID: 5010878

[…] examining the relationship between gene length and the number of identified variations was performed using stata 12.0 (stata, college station, tx)., we performed variant annotation using the ensembl variant effect predictor (vep) v. 74, build39, 40 and snpeff41 v. 3.5c (build 2014‐02‐21), annotated against the grch37.71 database, and restricted annotations to the ensembl canonical transcript […]

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).

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