VEGAS pipeline

VEGAS specifications

Information


Unique identifier OMICS_07065
Name VEGAS
Alternative name Versatile Gene-based Association Study
Interface Web user interface
Restrictions to use None
Input data Association results as a text file with two columns.
Input format GWAS
Output data The gene-based output is a plain-text file with the columns: Chromosome, Gene, Number of SNPs, Number of simulations, Start position, Stop position, Gene-based test statistic, P-value, Top-SNP, Top-SNP pvalue. The pathway-based output is also a plain-text file with the columns: GO_ID, Description, Pathway length, Pathway length after first cut, Pathwal length after second cut, Final pathway length, Combined p-value, Emipirical p-value, Genelist.
Programming languages Perl, R
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Subtool


  • VEGAS2Pathway

Maintainer


  • person_outline Aniket Mishra <>

Information


Unique identifier OMICS_07065
Name VEGAS
Alternative name Versatile Gene-based Association Study
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Association results as a text file with two columns.
Input format GWAS
Output data The gene-based output is a plain-text file with the columns: Chromosome, Gene, Number of SNPs, Number of simulations, Start position, Stop position, Gene-based test statistic, P-value, Top-SNP, Top-SNP pvalue. The pathway-based output is also a plain-text file with the columns: GO_ID, Description, Pathway length, Pathway length after first cut, Pathwal length after second cut, Final pathway length, Combined p-value, Emipirical p-value, Genelist.
Operating system Unix/Linux, Mac OS
Programming languages Perl, R
Computer skills Advanced
Stability Beta
Requirements mvtnorm, corpcor, plink2
Maintained Yes

Subtool


  • VEGAS2Pathway

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Maintainer


  • person_outline Aniket Mishra <>

Publications for Versatile Gene-based Association Study

VEGAS IN pipelines

 (13)
2018
PMCID: 5845532
PMID: 29559957
DOI: 10.3389/fendo.2018.00075

[…] of 25 query snps (p < 1 × 10−5) was submitted. the enrichments of cell-type enhancers with uncorrected p < 0.05 were reported., we performed gene-based tests on gwas summary results by using versatile gene-based association study-2 (vegas2) which uses 1,000 genomes data to model snp correlations across the autosomes and chromosome x (30, 31). in the test, the evidence for association […]

2018
PMCID: 5845532
PMID: 29559957
DOI: 10.3389/fendo.2018.00075

[…] the enrichments of cell-type enhancers with uncorrected p < 0.05 were reported., we performed gene-based tests on gwas summary results by using versatile gene-based association study-2 (vegas2) which uses 1,000 genomes data to model snp correlations across the autosomes and chromosome x (30, 31). in the test, the evidence for association from all snps was aggregated within a per […]

2016
PMCID: 4773746
PMID: 26901225
DOI: 10.3390/cancers8020023

[…] a polar and uncharged serine residue to a nonpolar uncharged proline. snpeffect analysis indicated this amino acid substitution may have a deleterious effect on protein function., we further used vegas to perform gene-based tests to summarize the effect of snps within a single gene on toxicities (table 6). in total, 7 genes (exo1, rpa1, mdc1, blm, rad54l, brca1, prkdc) were significantly […]

2016
PMCID: 5068862
PMID: 27489002
DOI: 10.1534/genetics.116.188391

[…] et al. 2016); regression-based methods such as the sequence kernel association test (skat) family of tests (wu et al. 2010, 2011) and stratified ld score regression (finucane et al. 2015); and vegas (liu et al. 2010) and raremetals (liu et al. 2013), which correct for linkage disequilibrium (ld) between snps, using simulations from a multivariate normal distribution whose variance […]

2016
PMCID: 5068862
PMID: 27489002
DOI: 10.1534/genetics.116.188391

[…] from a multivariate normal distribution whose variance is the empirical ld observed among snps within each gene being analyzed. multiple methods exist that use the same null distribution as vegas (tzeng and zhang 2007; pan 2009). other methods that have been proposed include fisher’s combination test (where the gene score must be calculated empirically using permutation tests), simes’ […]

VEGAS institution(s)
Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
VEGAS funding source(s)
This work was supported by an ANZ Trustees PhD scholarship, the Australian National Health and Research Council and Australian Research Council fellowships.

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