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

Emily L Webb; Gabrielle S Sellick; Richard S Houlston

doi:10.1093/bioinformatics/bti449

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

Bioinformatics. 2005 Jul 1;21(13):3060-1. doi: 10.1093/bioinformatics/bti449. Epub 2005 Apr 19.

Authors

Emily L Webb¹, Gabrielle S Sellick, Richard S Houlston

Affiliation

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

PMID: 15840706
DOI: 10.1093/bioinformatics/bti449

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Artificial Intelligence
Chromosome Mapping / methods*
Computer Simulation
DNA Mutational Analysis / methods*
Linkage Disequilibrium / genetics*
Models, Genetic
Models, Statistical
Polymorphism, Single Nucleotide / genetics*
Software*
Statistical Distributions
User-Computer Interface*