GenCall,43 Birdseed44 and zCall45 were used supplementary to improve variant calls. GenCall and Birdseed are genotype calling algorithms best suited for common variants, while zCall is a post-processing step for GenCall to improve genotype calling for rare variants. Approximately half of the probes on the array are common variants (minor allele frequency⩾0.05), while the other half are rare variants (minor allele frequency<0.05). A large subgroup of the rare variants are non-polymorphic within the cohort. A consensus genotype call was made from the three calling algorithms (Supplementary Text 2) using PLINK.46, 47
