GENECLUSTER is a novel program for detecting association in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes). The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the simulation program HAPGEN, and the input of the association analysis program SNPTEST.
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Z. Su, N. Cardin, WTCCC, P. Donnelly, J. Marchini (2009)
A Bayesian method for detecting and characterizing allelic heterogeneity and boosting signals in genome-wide association studies.
Statistical Science 24(4) 430-450