single-tile score reflecting the relative likelihood of the two possible parental origin assignments (score > 0 supporting one assignment and score < 0 supporting the other assignment, see Methods for details). We then tried to stitch the haplotypes from consecutive tiles together based on sharing at the overlapping region. Stitching and parental origin determination are complementary tasks. Specifically, if parental origin is determined with high confidence for one tile the information can be propagated to other tiles through stitching (Supplementary Figure 1A). Conversely, in cases where the overlap between two adjacent tiles is homozygous for all SNPs, stitching can still be accomplished if parental origins can be determined for both tiles independently (Supplementary Figure 1B). For haplotypes derived by stitching, a contig-score for parental origin is computed by summing the individual single-tile scores.
