Haploview
From Wikipedia, the free encyclopedia
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
[edit] References
- ^ 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. http://bioinformatics.oxfordjournals.org/cgi/reprint/21/2/263?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=haploview&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT.
- ^ 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. http://www.nature.com/ng/journal/v37/n11/pdf/ng1669.pdf.
