Rapid haplotype inference for nuclear families
1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA
2 David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA, 02142, USA
Genome Biology 2010, 11:R108 doi:10.1186/gb-2010-11-10-r108Published: 29 October 2010
Hapi is a new dynamic programming algorithm that ignores uninformative states and state transitions in order to efficiently compute minimum-recombinant and maximum likelihood haplotypes. When applied to a dataset containing 103 families, Hapi performs 3.8 and 320 times faster than state-of-the-art algorithms. Because Hapi infers both minimum-recombinant and maximum likelihood haplotypes and applies to related individuals, the haplotypes it infers are highly accurate over extended genomic distances.