Fourth, we use the surrogate maternal and paternal haplotypic assignments of probable IBD regions to make phase calls. Whenever at least one surrogate is homozygous at a proband het, we use that surrogate to phase the site. If all surrogates are also heterozygous, we make a probabilistic phase call based on the allele frequency of the SNP and the difference between the numbers of (heterozygous) surrogate maternal haplotypes and surrogate paternal haplotypes.
