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Bioinformatics Advance Access originally published online on April 19, 2005
Bioinformatics 2005 21(13):3060-3061; 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{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

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 before carrying out linkage analysis. SNPLINK can compute both parametric and non-parametric statistics, utilizing 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

Contact: richard.houlston{at}icr.ac.uk


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