Genetic maps were supplied with the Affymetrix GeneChip® Mapping 10k Array data set to CIDR. SNPs were mapped to unique physical positions on NCBI genome build 34 and interpolated onto one of two framework genetic maps: deCode [29] and Marshfield [30]. Because those framework maps contain multiple microsatellite markers at the same genetic location, interpolation onto these maps can cause non-unique SNP positions. We therefore removed all but one microsatellite marker at each genetic location to create a non-redundant framework, allowing all SNPs with unique physical positions to also have unique interpolated genetic positions [31]. These maps are periodically updated on new versions of the NCBI human genome sequence and are located on the Affymetrix NetAffx website for download [32].
