We chose not to employ a minor allele frequency (MAF) cutoff in any of the heritability analyses. This decision was based on the observation that minor allele frequency cutoffs did not alter estimates of heritability for the control-control analysis after establishment of stringent differential missingness rates and call rate. We partitioned the directly genotyped and imputed variants according to MAF bin. For the directly genotyped variants we created six bins representing MAFs from 0.001–.05, >0.05–0.1, >.1–.2, >.2–.3, >.3–.4, and >.4–.5 and generated GRMs for each bin. For the imputed genotypes we created two bins representing MAF 0.001–0.05 and >0.05 to 0.5 and generated GRMs for each bin. For each set of variants (directly genotyped and imputed respectively) we then combined binned GRMs in a single joint REML analysis, allowing the effects of LD to be partitioned by the REML analytic approach.
