We used our SHAPEIT2+duoHMM method to flag sites of possible genotyping error and then re-calculated the SE rates for SHAPEIT2+duoHMM and the Beagle Duo/Trio method excluding these sites. The results are shown in the last two rows of Table 2. Comparing these results to the unmasked results we see that the reduction in SE is greatest for SHAPEIT2+duoHMM, suggesting that genotyping error causes the results of Beagle Duo/Trio to appear better than they are. The results from our simulation study (described next) corroborate this point. Figure 4 (right) shows in more detail the effect of masking genotyping errors, and that SHAPEIT2+duoHMM outperforms Beagle Duo/Trio for individuals that were phased as ‘unrelated’ by Beagle.
