VEP statistics

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VEP specifications

Information


Unique identifier OMICS_00139
Name VEP
Alternative names Variant Effect Predictor, Ensembl 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 names Variant Effect Predictor, Ensembl 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


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Versioning


No version available

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 citations

 (312)
library_books

Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

2018
BMC Genet
PMCID: 5948690
PMID: 29751743
DOI: 10.1186/s12863-018-0620-0

[…] the first round, and these SNPs are in high LD with the two known causative polymorphisms in DGAT1 [], BTA14: 1802265 (rs109234250) and BTA14: 1802266 (rs109326954) (Additional file : Figure S1). The variant effect predictor (VEP) [] annotation showed these two variants in DGAT1 are missense mutations. The second strongest association signal was located on chromosome 5 with lead SNP, BTA5: 9394835 […]

library_books

Genetic alterations analysis in prognostic stratified groups identified TP53 and ARID1A as poor clinical performance markers in intrahepatic cholangiocarcinoma

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

[…] or 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), SnpSift, the Variant Effect Predictor (VEP) software and NCBI RefSeq database. Confident somatic mutations were obtained from annotated variants by: i) filtering-out germline mutations identified in matched normal […]

library_books

Human local adaptation of the TRPM8 cold receptor along a latitudinal cline

2018
PLoS Genet
PMCID: 5933706
PMID: 29723195
DOI: 10.1371/journal.pgen.1007298

[…] informatics tools to investigate possible functional effects of rs10166942 and it neighboring variants in high linkage disequilibrium (LD). We explored the predicted effects on protein sequence using variant effect predictor (VEP) [], focusing on the non-synonymous and splice-site SNPs, as well as indels annotated in the 1KGP. We explored effects on gene expression using Regulome DB annotations [] […]

library_books

Multi omics profiling of younger Asian breast cancers reveals distinctive molecular signatures

2018
Nat Commun
PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] aired mutation calling mode. Parameters were selected based on the DREAM-3 setting of the false positive filter as recommended by Varscan2. All germline and somatic mutations were annotated using the Ensembl Variant Effect Predictor. Significantly mutated gene analysis was performed using MutSigCV v1.2 from the online GenePattern tools. We used GATK to estimate depth of coverage from the bam files […]

library_books

Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

2018
Front Genet
PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] To predict the deleterious nature of the mutants, we employed dbNSFP at Ensemble VEP (Variant Effect Predictor) (McLaren et al., ) which produces prediction scores for different algorithms like SIFT, PolyPhen 2.0, CADD, FATHMM, LRT, MetaLR, MetaSVM, PROVEAN, and Condel. These tools wor […]

library_books

Genome Wide Association Analysis of Age Dependent Egg Weights in Chickens

2018
Front Genet
PMCID: 5932955
PMID: 29755503
DOI: 10.3389/fgene.2018.00128

[…] ariates to univariate and multivariate models to elucidate independent signals in step-wise conditional analyses. Annotations of candidate genes adjacent to significant SNPs were determined using the variant effect predictor (VEP) (McLaren et al., ) supplied by Ensembl (http://www.ensembl.org).We calculated SNP-based heritability (hsnp2) (Lee et al., ) and pairwise genetic correlations of EW trait […]

Citations

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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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