In general, MCMC software trades these memory requirements for substantially greater CPU usage. We thus chose LOKI for IBD matrix generation, but this software requires a choice of run length (number of iterations). The initial tests to determine an appropriate number of iterations for the generation of IBD matrices with LOKI shows that the higher density of the SNP maps greatly slows the MCMC process. In particular, while 10,000 iterations for microsatellites shows only slightly higher average variance of phi2 than one 100,000 iterations, the variance for SNPs is still quite high with 100,000 iterations. We ultimately used 1,000,000 iterations for the SNP datasets. Figures 1 and 2 show that 1,000,000 iterations for the SNP map produces about the same variance of phi2 as 10,000 iterations of the microsatellite map. However, there are still peaks of high variance, especially in the Affymetrix map.
