Phase

Description

PHASE v 2.0 is a program implementing the method for reconstructing haplotypes from population data

Usage

Command is:

   PHASE2.big

Old phase is still PHASE.big

What's new in v 2.0?

* faster haplotype estimates, particularly for large data sets.
* more accurate haplotype estimates, that take into account the decay of linkage disequilibrium with distance.
* the facility to estimate recombination rates along the genotyped region, and to identify potential recombination hotspots.

Descriptions of the extensions to the method can be found in references [2] and [3] below, and in the appendix to the instructions, which can be downloaded below.

Example input files

test.inp
test.casecontrol.inp
test2.inp
eg.known
eg.delta

Results

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Author

Algorithm by Matthew Stephens, Nicholas J. Smith, and Peter Donnelly.

Code by Matthew Stephens, with contributions from Na Li.

References

[1] 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. (link to article here, AJHG)

[2] Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, To appear. (PDF file here)

PHASE v 2.0 also allows recombination rates to be estimated along a region, as described in

[3] Li, N., and Stephens, M. (2003). Modelling Linkage Disequilibrium, and identifying recombination hotspots using SNP data Genetics, To appear. (PDF file here)

If you use haplotype estimates from the software in publications, please cite [1] and [2] above. If you also use estimates of the recombination rates, please also cite [3] above. In all cases, please specify the version of the software used, and any deviations from the default options.

Documentation

PHASE v.2.0 documentation/instructions (PDF file here)

Webpage

http://www.stat.washington.edu/stephens/software.html