RAPID is a software package that allows one to compute pairwise identity by descent (IBD) probabilities in very large pedigrees. It also performs linkage analysis using the S_pairs statistic given a set of affected individuals.

To install, go into the Src directory and read the file INSTALL.

For documentation, you can find the following files in the Doc directory:

usage - Instructions on using RAPID.

file_formats - An explanation on input file formats.

To try a simple analysis, read the Tutorial in the Example directory.

All files in this software package, unless specified otherwise, are copyright Mark Abney and licensed under the GPL v3 (see http://www.gnu.org/licenses).

Downloads

I have available a package with complete source code, documentation and example. The documentation and example are available only in this package. Also, a limited number of precompiled binaries are posted in gzip compressed format. Although these binaries were compiled with the ATLAS numerical library, they are optimized for the specific platform on which they were built. They will almost surely will not work as well (or, perhaps, even at all) on a different platform. I recommend installing ATLAS and building RAPID yourself, as described in the INSTALL file (it’s really not that hard!).

Source code and binaries for linux and Mac (PPC) can be downloaded from here.

Citation

Abney, Mark (2008) Identity by descent estimation and mapping of qualitative traits in large, complex pedigrees. Genetics 179:1577-1590

If you are interested in a copy of this manuscript, please email me at abney (at) uchicago edu.

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Updated July 25, 2008