PHASE

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PHASE is software for haplotype reconstruction, and recombination rate estimation from population data. The software implements methods for estimating haplotypes from population genotype data described in:

  • Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73:1162-1169.
  • Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978--989.
  • Stephens, M., and Scheet, P. (2005). Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. American Journal of Human Genetics, 76:449-462.


The software also incorporates methods for estimating recombination rates, and identifying recombination hotspots:

  • Crawford et al (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics

Documentation on the usage of PHASE can be downloaded here.

Project website: http://depts.washington.edu/uwc4c/express-licenses/assets/phase/

Load SGE module

The following Modules files should be loaded for this package:

module load phase/phase
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