ArticleBMC bioinformatics2014
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- HaploTypo: a variant-calling pipeline for phased genomes.Bioinformatics (Oxford, England) · 2020Article
- Unzipping haplotypes in diploid and polyploid genomes.Computational and structural biotechnology journal · 2020Review
- A New Fast Phasing Method Based On Haplotype Subtraction.The Journal of molecular diagnostics : JMD · 2019Article
- Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.Molecular biology and evolution · 2016Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe haplotype phasing problem tries to screen for phenotype associated genomic variations from millions of candidate data. Most of the current computer programs handle this problem with high requirements of computing power and memory. By replacing the computation-intensive step of constructing the maximum spanning tree with a heuristics of estimated initial haplotype, we released the WinHAP algorithm version 1.0, which outperforms the other algorithms in terms of both running speed and overall accuracy.
resultsThis work further speeds up the WinHAP algorithm to version 2.0 (WinHAP2) by utilizing the divide-and-conquer strategy and the OpenMP parallel computing mode. WinHAP2 can phase 500 genotypes with 1,000,000 SNPs using just 12.8 MB in memory and 2.5 hours on a personal computer, whereas the other programs require unacceptable memory or running times. The parallel running mode further improves WinHAP2's running speed with several orders of magnitudes, compared with the other programs, including Beagle, SHAPEIT2 and 2SNP.
conclusionsWinHAP2 is an extremely fast haplotype phasing program which can handle a large-scale genotyping study with any number of SNPs in the current literature and at least in the near future.
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