two properties. Firstly, for the same absolute difference between m(T,H) and f(T,H), the absolute value of score(T,H) is higher when the minimum of m(T,H) and f(T,H) is smaller, thus giving more weight to situations when a close relative who shared a haplotype is found. Secondly, the scoring was designed to be robust so that the result from one haplotype in one tile could not completely dominate the contributions from other haplotypes and adjacent tiles when results were combined (see below). When haplotypes for n consecutive tiles, T1,…,Tn, could be stitched together to form A = (A1,…,An) and B = (B1,…,Bn), then the contig score for parental origin assignment was calculated as contig-score(T1,…,Tn)=Σi=1,…,nscore(Ti). Parental original were assigned based on whether the contig-score was greater or smaller than zero. Most importantly, the accuracy of this procedure was evaluated using the trio test.
