metaGWASmanager: A toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia

Abstract

SummaryThis paper introduces the metaGWASmanager, which streamlines genome-wide association studies within large-scale meta-analysis consortia. It is a toolbox for both the central consortium analysis group and participating studies to generate homogeneous phenotypes, minimize variance from inconsistent methodologies, ensure high-quality association results, and implement time-efficient quality control workflows. The toolbox features a plug-in-based approach for customization. ResultsThe metaGWASmanager toolbox has been successfully deployed in both the CKDGen and MetalGWAS Initiative consortia across hundreds of participating studies, demonstrating its effectiveness in improving the efficiency of GWAS analysis by automating routine tasks and ensuring the value and reliability of association results, thus, ultimately promoting scientific discovery. AvailabilityGitHub: https://github.com/genepi-freiburg/metaGWASmanager Contactpschlos3@jhu.edu, matthias.wuttke@uniklinik-freiburg.de