The PCA module (Supplementary Section S2) fulfils two objectives (Supplementary Fig. S3): Identify and remove duplicated or related samples for case-control and trio cohorts;Assess ancestral outliers and population stratification with EIGENSTRAT (Price et al., 2006);Principal component scores are computed and could be utilized for visualization or as covariates to adjust for population structure in downstream post-imputation GWAS.
