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


Webb, EL; Sellick, GS; Houlston, RS; (2005) SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. Bioinformatics (Oxford, England), 21 (13). pp. 3060-1. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bti449

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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 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.

Item Type: Article
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
PubMed ID: 15840706
Web of Science ID: 230255400021
URI: http://researchonline.lshtm.ac.uk/id/eprint/2420

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