WinHAP

WinHAP phases haplotypes from population-scale genotype data using heuristic and divide-and-conquer strategies to enable efficient large-scale SNP phasing.

Key Features:

• Efficiency: Reduces computational resource requirements for haplotype phasing, enabling analysis of large-scale population genotype datasets on limited hardware.
• Speed: Employs heuristic methods and algorithmic optimizations, with WinHAP2 using a divide-and-conquer strategy to accelerate processing.
• Memory Usage: WinHAP2 can phase 500 genotypes with up to 1,000,000 SNPs using approximately 12.8 MB of memory.
• Parallel Computing: Integrates OpenMP for parallel processing to increase throughput compared with programs such as Beagle, SHAPEIT2, and 2SNP.
• Running Time: Can complete representative phasing tasks in approximately 2.5 hours on a standard personal computer.
• Accuracy: Maintains high overall phasing accuracy and is reported to outperform other algorithms in the field.

Scientific Applications:

• Large-scale genotyping studies: Suited for phasing datasets with very large SNP counts, including datasets with up to 1,000,000 SNPs.
• Phenotype-associated variant screening: Enables screening of phenotype-associated genomic variations from extensive genotype datasets.

Methodology:

Implements heuristic methods, a divide-and-conquer strategy, algorithmic optimizations, memory usage reduction, and OpenMP-based parallelization (WinHAP2).