Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Fig 2
In the first two steps we identify IBD segments and compile a list of potential sources for each one. In the iterative phase, we alternate between choosing sources for each IBD and grouping the IBDs that are placed within each individual. If the IBDs assigned to an individual can be arranged into two haplotypes meeting thresholds for coverage defined in Methods, then those haplotypes are considered strong. IBD segments that conflict with strong haplotypes are rejected and must be assigned a different source. When we are no longer building more haplotypes, we return the reconstructed chromosomes.