Figure S24 plots the SE rates on the simulated pedigrees for Beagle Duo/Trio SE rates of all individuals versus those of SHAPEIT2 (left) and SHAPEIT2+duoHMM (centre). The plot shows that the most accurate haplotypes are attained by the SHAPEIT2+duoHMM approach, and that the duo/trio constrained phasing can be susceptible to genotyping error. The SE rates of SHAPEIT2, SHAPEIT2+duoHMM and Beagle Duo/Trio were 0.104%, 0.065% and 0.269% respectively. When we removed sites flagged as genotyping errors by our method the SE rates were 0.073%, 0.034% and 0.231% respectively, suggesting that the masking can remove switch errors caused by genotyping errors.
