Rapid haplotype inference for nuclear families

Table 1 Runtime results comparing Hapi to other family-based haplotyping algorithms

Runtimes for maximum likelihood haplotyping using Hapi, Merlin Allegro and Superlink of nuclear families from the Huntington's Disease Venezuela Collaborative Study [32]. We list times for haplotyping all nuclear families and for haplotyping those with three or fewer children. *Superlink failed to haplotype the family with 11 children; we therefore used only 8 of the children from the 11 child family to time it. Times are averages from running Hapi eight times and Merlin, Allegro, and Superlink three times each. Runtimes also on a different machine for minimum-recombinant haplotyping using Hapi (averaged from eight runs) and PedPhase ^†for chromosome 1 only.

ISSN: 1474-760X