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Bioinformatics Advance Access published online on April 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti449
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 4, 2005
Revised April 8, 2005
Accepted April 11, 2005

Applications note

SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal

Emily L. Webb 1, Gabrielle S. Sellick 1, and Richard S. Houlston 1*

1 Section of Cancer Genetics, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK

* To whom correspondence should be addressed.
Richard S. Houlston, E-mail: richard.houlston{at}icr.ac.uk


  Abstract

Summary: SNPLINK is a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets. The presence of linkage disequilibrium (LD) between closely spaced SNP markers can falsely inflate linkage statistics. SNPLINK removes LD from the marker sets in an automated fashion and then carries out linkage analysis after LD has been removed. SNPLINK can compute both parametric and non-parametric statistics, utilising the freely available Allegro and Merlin software. Graphical outputs of whole genome multipoint linkage statistics are provided allowing comparison of results before and after the removal of LD.

Availability: SNPLINK is freely available for non-commercial research institutions. For full details see www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm.


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