shared between individuals in the reference panel and those in the study sample increases gradually as the size of the reference panel increases. For example, mosaic fragments used to reconstitute the FUSION samples using the individuals in the 500-sample reference panel were slightly >1 Mb long on average. These long stretches are easier for our Markov model to identify and are also likely to descend from a more recent common ancestor. This means they will have undergone fewer rounds of gene conversion and mutation, which gradually erode haplotype similarities and reduce the quality of our imputed genotypes. Overall, our results suggest that either genotyping a number of the study samples for markers of interest or increasing the size of the public reference panels will greatly improve the quality of genotype imputation.
