Individual genotype information was available for each subject. The Ricopili pipeline16 (https://github.com/Nealelab/ricopili) was used for the QC and imputation of the case-control cohorts. Most family-based cohorts were analyzed with the Picopili pipeline17 (https://github.com/Nealelab/picopili), which is designed to conduct genome-wide meta-analyses accounting for family structure. The genetic data from the Collaborative Studies on the Genetics of Alcoholism were imputed independently as previously described18 because of the need in that study to merge data on members of large multiplex families who were genotyped across multiple genotyping arrays.
