We predict that further advances in haplotype accuracy are possible. Firstly, it has recently been shown by ourselves and others that leveraging phase information in sequencing reads can lead to improved genotype calls and haplotype sets with lower switch error. In parallel work [11], we have extended SHAPEIT2 to utilize phase informative reads after genotypes have been called, and have shown that this improves phasing accuracy. Other authors [12, 13] have recently shown that joint inference of genotypes and haplotypes can improve both genotype and haplotype calls. However, it is yet to be determined how such improvements translate into downstream imputation accuracy. It is more likely that downstream imputation accuracy can be improved by increasing sample size of the reference panel. Efforts are now under way to create larger sets of haplotypes by combining together many low-coverage sequencing studies.
