Haplotyping via minimum recombinant paradigm

BACKGROUND: Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium. METHODS: Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree. RESULTS: The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute. CONCLUSION: Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.