HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).
|Tags||Scientific/Engineering Bioinformatics Medical Science|
|Operating Systems||Mac OS X OS Independent Unix|
Release Notes: This version is a port to the SNPFile version 2.0 format.
Release Notes: This version adds an option for restricting the MCMC search to a sub-interval of the full data. This is especially useful for SNPFile data, where the regions can be very wide, but where convergence and mixing can be very poor.
Release Notes: This version changes the --additive option to --allelic (since this is more accurate) and documents the option in the man pages.
Release Notes: This version adds a new likelihood function for (near-)additive disease models, increasing the power for detecting association for such diseases.
Release Notes: This version enables sampling of genotypes of the disease status, writing these samples to a file in the form of a matrix. Missing phenotypes have also been added. Individuals with missing phenotype are clustered together with all other individuals, but they are not used in the likelihood calculation.