Figure 4.
Imputation accuracy (genotype R2) of imputation protocols using random splitting of Haplotype Reference Consortium (HRC) panel as query and reference. The x-axis shows the minor allele frequency bins of the untyped variants. Each box plot shows the genotype-level R2 distribution of imputed variant genotypes. Phased and unphased protocols were run with and without augmentation (augment/no augment), as indicated in the legend. The central protocol corresponds to running Beagle with no protection mechanisms.
