We also find the duoHMM method is beneficial to Beagle and HAPI-UR when used to correct those haplotypes. For example the SE rate for HAPI-UR drops from 7.722% to 6.193% for the Split cohort. Table S3 gives the average number and type of correction applied to each cohort for each method. SHAPEIT2's haplotypes require less than 0.5 corrections on average for chromosome 10, this is consistent with the very small improvement in SE.
