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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

 (32)
library_books

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

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

[…] 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 […]

library_books

Identifying noncoding risk variants using disease relevant gene regulatory networks

2018
PMCID: 5816022
PMID: 29453388
DOI: 10.1038/s41467-018-03133-y

[…] further test the discriminative power of the network-based features, we built a random forest (rf) classifier using these features and sequence-based features used by two state-of-the-art methods, genome-wide annotation of variants (gwava) and funseq2. we evaluated the relative importance of all features (six from this study and 182 from gwava and funseq2 combined) by using a recursive feature […]

library_books

Putative functional genes in idiopathic dilated cardiomyopathy

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

[…] 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.. […]

library_books

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

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

[…] of the genome []., taking advantage of these valuable resources, multiple computational approaches have already been developed to annotate genetic variants using genome-wide profiling data including gwava [], cadd [], genocanyon [], eigen, eigenpc [], dann [], fitcons [], fathmm [], deltasvm [], dbnsfp [], funseq 2 [] and icages []. a common feature of those methods […]

library_books

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

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

[…] 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., , bram p. prins and karoline b. kuchenbaecker […]

library_books

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

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

[…] 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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