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. 2014 Apr 17;10(4):e1004234. doi: 10.1371/journal.pgen.1004234

Figure 4. Switch error rates for individuals in extended pedigrees for different phasing pipelines across all European cohorts (chromosome 10).

Figure 4

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.