We used release 21 of the HapMap data for which phased haplotypes are available in NCBI b35 coordinates. The SNPs that occur on each genotyping chip were obtained from the websites of Affymetrix and Illumina respectively. Some of the SNPs in these sets do not occur in the HapMap phased haplotype data due to QC measures applied to the raw genotype data. For the Affymetrix 6.0 and Illumina 1 M chips 90.8% and 88.1% of the SNPs on these chips respectively are in this release in HapMap. This will have the effect of making our estimates of power slight underestimates of the true power.
