Improved haplotype phasing using identity by descent. B. L. Browning1,2,3, S. R. Browning2 1) Medicine, Division of Medical Genetics, University of Washington, Seattle, WA; 2) Biostatistics, University of Washington, Seattle, WA; 3) Genome Sciences, University of Washington, Seattle, WA.

   We present a new haplotype phasing method that achieves higher accuracy than existing methods. The method is based on the Beagle haplotype frequency model, but unlike the original Beagle phasing method, the new method incorporates genetic recombination, genotype error, and segments of identity by descent.
    We compared the new haplotype phasing method to Beagle (r1230) and to SHAPEIT version 2 (r778) using Illumina Human 1M SNP data for chromosome 20. We phased 44 HapMap3 CEU trio offspring together with subsets of Wellcome Trust Case Control Consortium 2 controls (n=650, 1300, 2600, 5200). Phase error was measured at trio offspring genotypes on chromosome 20 that have phase determined by parental genotypes. The SHAPEIT states parameter was set at 6400 in order to increase its phasing accuracy.
    The new haplotype phasing method produced haplotype switch error rates that were 20-25% lower than the error rates for the existing Beagle method and 1-7% lower than the error rates for SHAPEIT. The difference in switch error rates between the new method and SHAPEIT increased with increasing sample size.
    The new haplotype phasing method will be incorporated into version 4 of the Beagle software package (

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