Figure 4.

Phasing data are required to establish the cis or trans relationship of two nonadjacent variants (bold and underlined). A: The true diplotype describing an individual having one allele with two nonadjacent variants that are not found in the same allele of the homologous chromosome. B: Output from a variant caller. C: Interpretation of the output of the variant caller. In the presence of phasing data, the correct haplotypes are established. In the absence of phasing data, the cis or trans association of the two variants cannot be distinguished.