The task of phasing in isolated populations is some what of a special case, as individuals from such populations exhibit much higher levels of relatedness, and will tend to share much longer stretches of sequence identically by descent (IBD) than a pair of unrelated individuals from a non-isolated population. Kong at al.(2008) [12] proposed a method in which surrogate parents are identified for each individual in a given region of the genome. These surrogate parents allow the haplotypes to be determined with high accuracy using Mendelian inheritance rules, effectively as if the true parents had been observed and the family could be phased as a trio. More recently, a model based version of this approach called Systematic Long Range Phasing (SLRP) has been proposed [13]. Both of these papers demonstrated accurate haplotype estimates within IBD regions, but suffer from the problem that phase can only be inferred for genomic regions where IBD sharing is detected. Even in IBD regions, if a site is heterozygous in all individuals, the phase at that particular locus cannot be inferred.
