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Variant Effect Predictor VEP

Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the genes and transcripts affected by the variants, location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions), consequence of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift); known variants that match yours, and associated minor allele frequencies from the 1000 Genomes Project, SIFT and PolyPhen scores for changes to protein sequence.

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VEP forum

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VEP classification

  • Animals
    • Homo sapiens

VEP specifications

Interface:
Web user interface, Application programming interface
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Stability:
Stable

VEP distribution

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No open topic.

VEP classification

  • Animals
    • Homo sapiens

VEP specifications

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

VEP distribution

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VEP support

Documentation

Maintainer

  • William McLaren <>
This tool is not maintained anymore.

Additional information

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

Credits

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Publications

Institution(s)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

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).

Link to literature

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