Haploview

Haploview[1] is a commonly used bioinformatics software which is designed to analyze and visualize patterns of linkage disequilibrium (LD) in genetic data. Haploview can also perform association studies, choosing tagSNPs[2] and estimating haplotype frequencies. Haploview is developed and maintained by Dr. Mark Daly's lab at the MIT/Harvard Broad Institute.

Haploview currently supports the following functionalities:

  • LD & haplotype block analysis
  • Haplotype population frequency estimation
  • Single SNP and haplotype association tests
  • Permutation testing for association significance
  • Implementation of Paul de Bakker's Tagger tag SNP selection algorithm
  • Automatic download of phased genotype data from HapMap
  • Visualization and plotting of PLINK whole genome association results including advanced filtering options

References
  1. Barrett J.C.; Fry B.; Maller J.; Daly M.J. (2005). "Haploview: analysis and visualization of LD and haplotype maps". Bioinformatics. 21 (2): 263–5. doi:10.1093/bioinformatics/bth457. PMID 15297300.
  2. de Bakker P. I.; Yelensky R.; Pe'er I.; Gabriel S. B.; Daly M. J.; Altshuler D. (2005). "Efficiency and power in genetic association studies". Nature Genetics. 37 (11): 1217–23. doi:10.1038/ng1669. PMID 16244653.
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