Winkler TW Day FR Croteau-Chonka DC Wood AR Locke AE Mägi R Ferreira T Fall T Graff M Justice AE Luan J Gustafsson S Randall JC Vedantam S Workalemahu T Kilpeläinen TO Scherag A Esko T Kutalik Z Heid IM Loos RJ 2014 Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete. application/pdf https://sonar.ch/global/documents/106053 eng info:eu-repo/semantics/altIdentifier/doi/10.1038/nprot.2014.071 info:eu-repo/semantics/altIdentifier/pmid/24762786 info:eu-repo/semantics/openAccess Nature protocols. - 2014 Genome-Wide Association Study Meta-Analysis as Topic Quality Control Software Quality control and conduct of genome-wide association meta-analyses. http://purl.org/coar/resource_type/c_6501