After the datasets were combined and appropriate SNP and subjects filters applied, the compiled datasets were separately imputed. We used the 1000 Genomes Project ALL Phase I Integrated Release Version 3 Haplotypes excluding monomorphic and singleton sites (2010–11 data freeze, 2012-03-14 haplotypes) as the reference panel. SNP and indel genotypes were imputed in three steps. First, genotypes on each chromosome were split into chunks to facilitate windowed imputation in parallel using ChunkChromosome (v.2011-08-05). Then each chunk of chromosome was phased using MACH [50,51] (v.1.0.18.c). In the final step, Minimac (v.2012-08-15) was used to impute the phased genotypes to approximately 31 million markers in the 1000 Genomes Project.
