choose surrogate parent haplotypes. For each individual, we restrict the search space to 200 haplotypes that most closely match the two pre-existing haplotypes of the individual using a Hamming distance metric (100 for each haplotype). We run the method on chunks of 1,024 sites at a time, which is the default setting for SNPtools. Since the pre-existing haplotypes from each study do not contain exactly the same set of sites we filled in missing alleles in the pre-existing haplotypes at our site list using the major allele at each site.
