Dataset formats

The input datasets are in gd_snp, gd_genotype, and gd_indivs formats. The output dataset is in text format.

What it does

For each pair of individuals, one from each specified set, the program computes the expected heterozygosity of any offspring of the pair, i.e., the probability that the offspring has distinct nucleotides at a randomly chosen autosomal SNP. In other words, we add the following numbers for each autosomal SNP where both genotypes are defined, then divide by the number of those SNPs:

0 if the individuals are homozygous for the same nucleotide

1 if the individuals are homozygous for different nucleotides

1/2 otherwise (i.e., if one or both individuals are heterozygous)

A SNP is ignored if one or both individuals have an undefined genotype (designated as -1).