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. Author manuscript; available in PMC: 2016 Dec 6.
Published in final edited form as: Nat Genet. 2016 Jun 6;48(7):811–816. doi: 10.1038/ng.3571

Figure 1. Eagle algorithm and example phase calls after each step.

Figure 1

We show phase calls for ten trio children after each successive step of the Eagle algorithm (applied to phase the first 40cM of chromosome 10 in all N≈150,000 UK Biobank samples except trio parents). At all trio-phased sites, red and blue indicate whether the first Eagle-phased haplotype for each child matches the maternal or paternal haplotype. (a) After the first step, a sizable proportion of each genome is covered by long segments of near-perfect phase; these segments are the regions in which long IBD is available from several relatives. (b) The second step, which uses both long and short IBD, fixes most of the phase switch errors in the first step. (c,d) The subsequent approximate HMM iterations further reduce the error rate.