Previously2, we introduced the method of long range phasing that allows for accurate phasing of Icelandic samples typed with Illumina bead chips for regions up to10 cMs in length. Two advances have been made since then, stitching and parental origin determination. Genome-wide, long range phasing was applied to overlapping tiles, each 6 cM in length, with 3 cM overlap between consecutive tiles. For each tile, we attempted to determine the parental origins of the two phased haplotypes regardless of whether the parents of the proband were chip-typed. Using the Icelandic genealogy database, for each of the two haplotypes of a proband, a search was performed to identify, among those individuals also known to carry the same haplotype, the closest relative on each of the paternal and maternal sides (Figure 1). Results for the two haplotypes were combined into a robust 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
