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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

[…] 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 w […]


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

[…] nal 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. […]


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

[…] ies, 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. The […]


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

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

[…] 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 so that the […]


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

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

[…] ed 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 was used […]


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

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

[…] for 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 the […]


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

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