Data for the cohorts that shared raw genotypes were deposited to a secure server for uniform quality control (QC). QC and imputation of the 14 case/control studies was performed using the ricopili pipeline (https://github.com/Nealelab/ricopili). For the 9 family-based cohorts, an equivalent pipeline, picopili (https://github.com/Nealelab/picopili), was developed for QC, imputation, and analysis appropriate for diverse family structures, including twins, sibships and extended pedigrees (Supplementary Information A2).
