The HapMap 3 samples were genotyped on both the Affymetrix SNP 6.0 platform and the Illumina 1M Human platform. For our cross-validations, we masked the SNPs not typed on the Affymetrix platform in one individual at a time, then imputed the masked genotypes from the haplotypes of other HapMap 3 individuals; details about which individuals were included in the reference panel are provided below. We also masked the phase of the observed genotypes in the individual being imputed. For these experiments, we used all of the HapMap 3 SNPs on chromosome 20, which led to 16,606 non-Affymetrix SNPs being imputed from 19,650 Affymetrix SNPs. We also repeated the experiments after reversing the roles of the SNP platforms, with results shown in File S3.
