Overview of Parente2. A sliding block B of equal size to the minimum target size for IBD segment detection is examined, starting at every marker of the genome. In this figure, a block B of length 2 cM is displayed. The block contains windows, which are sets of winsize possibly nonconsecutive markers (by default, winsize = 8; in our benchmarks against other methods prior to optimizing this parameter, winsize = 5). A set of consecutive-marker windows tiles B; these are called the basic windows. In addition, c sets of nonconsecutive-marker windows tile B (by default, c = 10). Each such nonconsecutive window is generated by choosing winsize markers out of r markers (by default, r = 40; in this figure, r = 30). These are called the augmented windows. Windows are ordered lexicographically by their leftmost markers and grouped into window subsets by forming a subset out of each successive subsetsize window (by default, subsetsize = 5). Each window subset WSi is scored according to the outer log-likelihood ratio (Equation 6 in Methods) to yield ELRi; the score of B is the sum of these window subset scores according to Equation 7 in Methods.
