HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program developed by Scheet and Stephens (2006). The program models unphased genotype data on unrelated individuals, and fits a model in which linkage disequilibrium is generated by K independent Poisson arrival processes corresponding to K modal haplotype states. This corresponds to the observation that typically 2-4 common haplotypes account for most of the allelic diversity in any haplotype block, and that rarer haplotypes are typically slight variants of these modal haplotypes. The block-like structure of haplotypes in the genome, corresponding to ancestral recombination hotspots, is modelled by allowing the arrival rate to vary across the genome.
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