HaploRec

HaploRec reconstructs phased haplotypes from unphased genotypes of unrelated individuals to enable large-scale haplotype-based disease association and gene mapping studies.

Key Features:

• Phasing target: Reconstructs phased haplotypes from unphased genotypes of unrelated individuals, addressing the haplotype reconstruction (phasing) problem.
• Statistical models: Implements three statistical models that exploit local regularities conserved within haplotypes to maximize local coherence.
• Local independence assumption: Does not assume statistical dependence between markers located far apart, enabling treatment of sparse marker maps.
• Efficiency and scalability: Exhibits running times approximately linear in the number of subjects and markers, reported as several orders of magnitude faster than Phase on large datasets.
• Comparative performance: Outperforms or is competitive with methods such as Phase, fastPhase, PL-EM, Snphap, and Gerbil, particularly with sufficiently large sample sizes.

Scientific Applications:

• Gene mapping: Provides haplotype reconstruction suited for linkage and association mapping in sparse marker maps.
• Disease association studies: Enables large-scale haplotype-based association analyses to identify genetic variants linked to disease.
• Population genetics: Facilitates analysis of genetic patterns within and across populations through inferred haplotypes.

Methodology:

Uses three statistical models that exploit local regularities conserved within haplotypes to maximize local coherence and explicitly does not assume dependence between distant markers; reported running time scales approximately linearly with the number of subjects and markers.