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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

Download


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Versioning


No version available

Maintainer


  • person_outline Aniket Mishra

Publications for Versatile Gene-based Association Study

VEGAS citations

 (132)
library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] We performed gene-based association testing using the VEGAS2 software. VEGAS2 is an extension of the VErsatile Gene-based Association Study (VEGAS) approach that uses 1000 genomes reference data to estimate LD between variants and provides a test using a […]

library_books

A sibling method for identifying vQTLs

2018
PLoS One
PMCID: 5884517
PMID: 29617452
DOI: 10.1371/journal.pone.0194541

[…] ed (p = 0.0015 in the FHS data; p = 0.1 in the replication data). Table I in shows other significant gene sets identified using PASCAL that replicated at various p-value thresholds in the MTFS data. VEGAS1 yielded no further significant gene sets.i-GSEA4GWAS and PASCAL for pathway analysis each yielded some pathways that appeared to be significantly enriched (). One of these pathways, associated […]

library_books

A Meta Analysis of Genome Wide Association Studies of Growth Differentiation Factor 15 Concentration in Blood

2018
Front Genet
PMCID: 5876753
PMID: 29628937
DOI: 10.3389/fgene.2018.00097

[…] Gene-based association analysis was conducted in a hypothesis-free manner through applying the Versatile Gene-based Association Study (VEGAS) algorithm () to the genome-wide meta-analysis results of the discovery cohorts. SNPs within ± 10 kb of a gene were used in this analysis, and the results […]

library_books

Heritability and Genome Wide Association Analyses of Serum Uric Acid in Middle and Old Aged Chinese Twins

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

[…] (KCNQ1) by Li et al. () in Chinese populations.Even though none genome-wide significant genes were found, a total of 167 genes were observed to be nominally associated with SUA level (P < 0.05) from VEGAS2 analysis. The results of GO gene sets from using GSEA program indicated that these genes might be associated with process of generation, catabolism, transport, intracellular signal transduction […]

library_books

Genome wide pleiotropy analysis of neuropathological traits related to Alzheimer’s disease

2018
PMCID: 5819208
PMID: 29458411
DOI: 10.1186/s13195-018-0349-z

[…] ults from individual SNP tests. SNPs within 30 kb of the transcription start and end sites were included in each gene-based test. These analyses were carried out using the versatile gene-based test (“VEGAS”) method [], which computes an empirical P value through Monte Carlo simulations based on linkage disequilibrium patterns of the European ancestry population in the 1000 Genomes Project (GRCh37 […]

library_books

Prevention of Hepatitis B Virus Infection in the USA: Recommendations of the Advisory Committee on Immunization Practices

2018
PMCID: 5837403
DOI: 10.15585/mmwr.rr6701a1

[…] ers: Robert Atmar, MD, Baylor College of Medicine, Houston, Texas; Edward Belongia, MD, Marshfield Clinic Research Foundation, Marshfield, Wisconsin; Echezona Ezeanolue, MD, University of Nevada, Las Vegas, Nevada; Paul Hunter, MD, City of Milwaukee Health Department, Milwaukee, Wisconsin; Allison Kempe, MD, University of Colorado School of Medicine, Denver, Colorado; Grace Lee, MD, Boston Childre […]

Citations

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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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