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Bioinformatics Advance Access published online on April 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl153
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 8, 2006
Revised April 5, 2006
Accepted April 16, 2006

Applications note

GeneRecon--a coalescent based tool for fine-scale association mapping

Thomas Mailund 1 *, Mikkel H. Schierup 2, Christian N. S. Pedersen 3, Jesper N. Madsen 4, Jotun Hein 5, and Leif Schauser 2

1 Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark; Bioinformatics ApS, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark; Dept. of Statistics, University of Oxford, Oxford, OX1 3TG, UK
2 Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark; Bioinformatics ApS, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark
3 Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark; Bioinformatics ApS, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark; Dept. of Computer Science, University of Aarhus, IT-Parken, DK-8200 Århus N, Denmark
4 Bioinformatics ApS, Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark
5 Dept. of Statistics, University of Oxford, Oxford, OX1 3TG, UK

* To whom correspondence should be addressed.
Thomas Mailund, E-mail: mailund{at}birc.au.dk


  Abstract

Summary: GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and micro-satellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis Hastings sampling in the state space of genealogies. Input format, search strategy, and the sampled statistics can be configured through the Guile Scheme programming language embedded in GeneRecon, making GeneRecon highly configurable.

Availability: The source code for GeneRecon, written in C++ and Scheme, is available under the GNU General Public License (GPL) at http://www.birc.au.dk/~mailund/GeneRecon.

Associate Editor: Martin Bishop
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