Algorithms for Haplotype Phasing

A haplotype is the sequence of nucleotides along a single chromosome. As humans, we have 23 pairs of chromosomes. However, with current technology, it is di cult to separate the two chromosomes of a pair and we often get combined haplotype, or genotype, information. The objective of haplotype phasing is to resolve (phase) the haplotypes given genotype information. Knowing the haplotypes not only gives us a complete picture of an individual’s genome, but also has other significant biological motivations. Here we study how the haplotype phasing problem has been reformulated as technology to read the human genome has progressed. We also describe the algorithmic techniques used under the di↵erent formulations, and end by discussing the current state of the problem and future directions.