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Bioinformatics. 2005 Jul 1;21(13):3060-1. Epub 2005 Apr 19.

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

Author information

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

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.

PMID:
15840706
DOI:
10.1093/bioinformatics/bti449
[Indexed for MEDLINE]

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