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GWAtoolbox specifications


Unique identifier OMICS_04413
Name GWAtoolbox
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for GWAtoolbox

GWAtoolbox citations


1000 Genomes based meta analysis identifies 10 novel loci for kidney function

Sci Rep
PMCID: 5408227
PMID: 28452372
DOI: 10.1038/srep45040

[…] in the model. family-based studies accounted for relatedness using mixed effect models. details on the study-specific methods are reported in ., all gwas files underwent quality control using the gwatoolbox package. gwas meta-analyses for egfrcrea and egfrcys were performed using the software metal assuming fixed effects across studies and using inverse-variance weighting, excluding variants […]


Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta analysis of Genome Wide Association Studies

PLoS Genet
PMCID: 4766012
PMID: 26910538
DOI: 10.1371/journal.pgen.1005874

[…] quality control prior to meta-analysis. checking of file formatting, data plausibility, and distributions of test statistics and quality measurements was facilitated by the gwasqc function of the gwatoolbox package v1.0.0 in r []. prior to the meta-analysis, variants with low minor allele frequency (<1%) and poor imputation quality (r2< 0.4) were removed., meta-analysis was performed […]


Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function

Nat Commun
PMCID: 4735748
PMID: 26831199
DOI: 10.1038/ncomms10023

[…] for a total sample size of 117,165, including 12,385 ckd cases. gwas of egfrcys were comprised by 16 studies for a total sample size of 32,834. all gwas files underwent quality control using the gwatoolbox package in r, before including them into the meta-analysis. genome-wide meta-analysis was performed with the software metal, assuming fixed effects and using inverse-variance weighting. […]


Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation

Nat Commun
PMCID: 4686825
PMID: 26635082
DOI: 10.1038/ncomms9658

[…] the regression for ever-smoking status and used appropriate tests for association in related individuals, as described in the ., quality-control checks on the stage-1 data were undertaken using gwatoolbox and r version 3.0.2 (see urls). all meta-analysis steps were undertaken using inverse variance-weighted fixed-effects meta-analysis. effect estimates were flipped across studies […]


Genome wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes

PMCID: 4764151
PMID: 26631737
DOI: 10.2337/db15-1313

[…] as the dependent variable that was regressed on imputed allelic dosages for each snp in the gwas., before the meta-analyses, all study-specific gwas summary files underwent quality control using the gwatoolbox (). genomic-control (gc) () correction was applied when the gc factor was >1. inverse variance weighted fixed-effects meta-analyses were conducted using metal (). the i2 statistic […]


Genome wide association study of kidney function decline in individuals of European descent

PMCID: 4425568
PMID: 25493955
DOI: 10.1038/ki.2014.361

[…] the amish study, which provided data to egfrchange overall and egfrchange no ckd only due to low number of ckd cases at baseline and follow-up., all input files underwent quality control using the gwatoolbox package in r ( [], before including them into meta-analysis. study data was meta-analyzed assuming fixed effects and using inverse-variance weighting. thus […]

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GWAtoolbox institution(s)
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA

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