Fig. 1. Rationale of SHAPEIT5.

a, All samples are phased at common variants (MAF ≥ 0.1%). b, Phasing of a given rare variant onto the haplotypes at common variants. Conditioning haplotypes used in the estimation share long matches with the target (green and blue) and are not monomorphic at the rare variant. Since heterozygous genotypes for the rare variant are unphased, the minor alleles at those are assumed to be on both haplotypes (i.e., forcing homozygosity). c, Singleton phasing by assigning the new allele on the target haplotype with the shortest match. d, Compound heterozygous event mapping based on the rare variant phasing (a–c).