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A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

Figure 4

Switch error rates for individuals in extended pedigrees for different phasing pipelines across all European cohorts (chromosome 10).

Points are coloured according to what relationship was used by Beagle to phase that individual (red meaning no relationships were used). Left: Beagle using duo/trio phasing versus SHAPEIT2 using no relationships. Centre: Beagle using duo/trio phasing versus SHAPEIT2+duoHMM using no relationships. Right: Beagle using duo/trio phasing versus SHAPEIT2+duoHMM using no relationships when masking loci flagged as probable genotyping errors by the duoHMM. Switch error is reduced for both methods suggesting the masking is sensible.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1004234.g004