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A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
November 2003
November 2003
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Abstract
In this report, we compare and contrast three previously published Bayesian methods
for inferring haplotypes from genotype data in a population sample. We review the
methods, emphasizing the differences between them in terms of both the models ("priors")
they use and the computational strategies they employ. We introduce a new algorithm
that combines the modeling strategy of one method with the computational strategies
of another. In comparisons using real and simulated data, this new algorithm outperforms
all three existing methods. The new algorithm is included in the software package
PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html).