Although the Affymetrix map consists of more than twice as many SNPs as the Illumina map, increased density of SNPs in the Affymetrix map does not appear to provide more information. However, many of the SNPs in the Affymetrix map have fairly low heterozygosity [5]. We also observed that a subset of the Illumina map provided nearly as much information as the full map. Although the best solution for markers in LD is probably to modify existing software to haplotypic information, it appears that simply removing SNPs may be a useful interim procedure.
