HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory.
HapCluster++ 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 below (the original implementation was in R).
HapCluster++ is written in C++ and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
To build the source files, first uncompress and untar the file, then run 'configure' and finally 'make'. To test that the build was successful, run 'make check'. To install the program, run 'make install'.
$ tar zxf hapcluster-version.tar.gz
$ cd hapcluster-version
$ make check
$ make install
HapCluster++ is started on the command line, taking as input a file containing marker positions and a file containing phased haplotypes:
$ hapcluster positions.txt haplotypes.txt
The format of the haplotype file is: One line per haplotype, where a haplotype is represented as a list of space-separated alleles, and each allele represented as either a '0' or a '1'. The haplotypes are taken as pairwise genotypes, so for even numbers j the lines j and j+1 is taken as the haplotypes for individual j/2.
The first column is a 'pseudo'-allele used for the case/control dichotomy: a '0' in the first column is taken to mean that the haplotype is a control haplotype and a '1' at the first column is taken to mean that the haplotype is a case haplotype.
When run, the program outputs samples from the posterior density of disease loci. These samples can then be analysed in other software packages, such as e.g. R.
By default, samples of the disease locus is written to standard out, but this can be changed to a file using the option -o - this is especially recommended when running HapCluster in verbose mode (option -v).
Run hapcluster --help to get a complete list of command-line options accepted by HapCluster.
What's New in This Release:
· This version is a port to the SNPFile version 2.0 format.