3. This step involves the simulation of two new haplotypes for the individual conditional upon the alleles simulated at the disease locus in Step 2 and conditional upon the fine-scale recombination map across the region. This involves simulating the rest of hk+1 and hk+2. We only describe the generation of sites right flanking of the disease locus as the generation of the left flanking markers is virtually identical. Also the simulation of h k+2 follows directly from our description of how the rest of h k+1 is simulated.
