Author Summary Precise haplotype maps are preferred for the performance of a variety of genetic studies including identification of disease-associated loci and dissection of evolutionary mechanisms such as selection and recombination. For diploid organisms, the haplotype information appears as the genotypes when we obtain the information using widely used high-throughput techniques. The process of extracting haplotype information from genotypes is called phasing, which can be accurately done if the genotypes are from related individuals, such as parent–child trios, by considering the constraints imposed by the rules of Mendelian inheritance. For the genotype data without family information, phasing is done by one of the methods that are based on haplotype clustering, and the inferred haplotypes are known to be less accurate. Here, we experimentally determined genome-wide definitive haplotypes using a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. Using these resources, we asked if the definitive haplotype data can detect long-distance information that has been obscured when we rely solely on the haplotypes inferred by clustering. We also show that by introducing definitive haplotypes as references, inference of haplotypes of unrelated individuals is significantly improved.
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