GWAVA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GWAVA
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Tool usage distribution map

This map represents all the scientific publications referring to GWAVA per scientific context
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Associated diseases

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Protocols

GWAVA specifications

Information


Unique identifier OMICS_08572
Name GWAVA
Alternative name Genome Wide Annotation of VAriants
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Paul Flicek

Information


Unique identifier OMICS_08572
Name GWAVA
Alternative name Genome Wide Annotation of VAriants
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Paul Flicek

Publication for Genome Wide Annotation of VAriants

GWAVA citations

 (35)
library_books

Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets

2018
Sci Rep
PMCID: 5821758
PMID: 29467471
DOI: 10.1038/s41598-018-20721-6

[…] region containing the CAD-associated SNPs, and (3) the eQTL most significantly associated with the CAD lead SNP or proxy–. A “Prioritized Gene List” was generated as described in the Results section. GWAVA software was used to identify transcribed SNPs and SNPs that alter the coding sequence. Deleterious SNPs were predicted with SIFT, PolyPhen, and CADD. Mouse phenotypes were assigned if the gene […]

call_split

Identifying noncoding risk variants using disease relevant gene regulatory networks

2018
Nat Commun
PMCID: 5816022
PMID: 29453388
DOI: 10.1038/s41467-018-03133-y
call_split See protocol

[…] To classify risk eSNPs, we trained an RF classifier using the combined feature set that consists of 5 network-based features, 6 binary features from FunSeq, and 175 features from GWAVA. The classifier contained 500 decision trees. Each decision tree was built using ~20% of randomly selected training data (100 out of 464) and 187≈14 randomly selected features. Classification er […]

library_books

Putative functional genes in idiopathic dilated cardiomyopathy

2018
Sci Rep
PMCID: 5758757
PMID: 29311597
DOI: 10.1038/s41598-017-18524-2

[…] work called Combined Annotation Dependent Depletion (CADD) uses SVM to estimate relative pathogenicity of human SNPs. Polyphen-2 predicts damaging effects of missense mutations. Another method called GWAVA supports the prioritization of non-coding variants by using multiple epigenomic and genomic annotations. A Bayesian approach to detect potentially causal eQTL SNPs was proposed in Das et al.. A […]

library_books

Using DIVAN to assess disease/trait associated single nucleotide variants in genome wide scale

2017
BMC Res Notes
PMCID: 5663107
PMID: 29084591
DOI: 10.1186/s13104-017-2851-y

[…] r the order of GWAS p-values, which could be another important feature added into the training model. Other types of epigenomic features, including eQTL, DNA methylation, and pre-computed scores from GWAVA, CADD, and GenoCanyon could also be informative features to improve DIVAN further. […]

library_books

Genome wide analysis of health related biomarkers in the UK Household Longitudinal Study reveals novel associations

2017
Sci Rep
PMCID: 5591265
PMID: 28887542
DOI: 10.1038/s41598-017-10812-1

[…] ions from ENSEMBL, including variant function, the nearest gene IDs within < 500Kb from a given variant, transcript and protein IDs for these genes, as well as conservation scores. It also calculates GWAVA scores for non-genic variants amongst other annotations.All methods were performed in accordance with the relevant guidelines and regulations. […]

library_books

Genome wide Regional Heritability Mapping Identifies a Locus Within the TOX2 Gene Associated With Major Depressive Disorder

2017
Biol Psychiatry
PMCID: 5553996
PMID: 28153336
DOI: 10.1016/j.biopsych.2016.12.012

[…] h MDD. We then examined the functional role of the 38 SNPs using the following functional annotation tools and analyses: the potential to affect the binding of transcription factors in RegulomeDB (), Genome Wide Annotation of Variants (GWAVA), Genomic Evolutionary Rate Profiling (GERP) (), brain-tissue-specific allelic effect on gene expression (expression quantitative trait loci [eQTL] analysis) […]


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GWAVA institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK and Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

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