The pre-imputation/QC module (Supplementary Section S1) consists of the following general steps (Supplementary Fig. S2): Inferring the genotyping chip;Standardizing file names and sample identifiers, incorporating chip information and ensuring that sample IDs across distinct cohorts are unique while keeping original sample IDs intact;Carrying out technical sample and variant QC procedures: RICOPILI will assign red, yellow and green flags to various QC parameters to help with the decision if a cohort needs further work before going into the following modules (Supplementary Fig. S1.1).
