GWAMA protocols

GWAMA specifications

Information


Unique identifier OMICS_00235
Name GWAMA
Alternative name Genome-Wide Association Meta-Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Reedik Mägi <>

Publication for Genome-Wide Association Meta-Analysis

GWAMA IN pipelines

 (14)
2016
PMCID: 4856879
PMID: 26839038
DOI: 10.1038/ejhg.2016.1

[…] likely to favour success for trans-ethnic meta-analyses., in this simulation study, trans-ethnic meta-analysis was carried out by a frequentist fixed-effects meta-analysis that was implemented in gwama8 as a proof of principle in comparing fine-mapping of studies having varying degrees of ancestral diversity. in addition, for completeness, we also employed gwama using random effects […]

2016
PMCID: 4856879
PMID: 26839038
DOI: 10.1038/ejhg.2016.1

[…] that was implemented in gwama8 as a proof of principle in comparing fine-mapping of studies having varying degrees of ancestral diversity. in addition, for completeness, we also employed gwama using random effects in a selection of settings. fine-mapping assessment was examined when the variant had a non-null effect in all of the populations and under various levels of ancestral […]

2016
PMCID: 5072673
PMID: 27764105
DOI: 10.1371/journal.pone.0163877

[…] model, was performed using snptest v2 for both genotyped and imputed markers [64]. to combine the effect estimates from both studies, a fixed-effects meta-analysis was conducted for sciatica using gwama [65]. the presence of heterogeneity across studies was investigated with cochran’s q (weighted sum of squares) test and i2 statistic (percentage of true heterogeneity to total observed […]

2016
PMCID: 5438072
PMID: 27029810
DOI: 10.1038/ncomms11174

[…] pakistani 368. more details on the counts of subjects flowing through quality control are available in supplementary table 3., although our analysis followed the broad strategy of best practice gwama, the unique characteristics of our data set and, to a lesser extent, trait meant we modified the design slightly. all subjects were genotyped on only two, very similar, arrays. this meant […]

2015
PMCID: 4583479
PMID: 26406328
DOI: 10.1371/journal.pgen.1005535

[…] association analysis was performed by logistic regression under an additive model, implemented in snptest, and summary statistics from the ten studies aggregated by fixed-effects meta-analysis using gwama [20]., we performed these analyses using an unfiltered set of 1000 genome-derived genotypes, equivalent to an association study performed on genome-wide sequence data (“gold standard” […]

GWAMA institution(s)
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

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