Detecting Structure of Haplotypes and Local Ancestry

  title={Detecting Structure of Haplotypes and Local Ancestry},
  author={Yongtao Guan},
We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry of admixed individuals. Our method outperforms competing state-of-the-art methods, particularly for regions of small ancestral track lengths. Applying our method to Mexican samples in HapMap3… CONTINUE READING
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