HAF: Haplotype Allele Frequency.

A haplotype ‘contains/carries a mutation e’ if it has the derived allele at site e. Recently, we devised the HAF score to capture the dynamics of a selective sweep⁶. The HAF score for a haplotype h (HAF(h)) is the sum of the derived allele counts of the mutations on h (see Supplementary Note 1; Fig. 1a). It has been shown that, when h is a carrier of the favored allele, HAF(h) increases with the frequency of the favored mutation (Equation SN1.9 of Supplementary Note 2), in contrast to HAF scores of non-carriers (Equation SN1.10 of Supplementary Note 2), and this can be used to separate carrier haplotypes from non-carriers without knowing the favored mutation⁶.