SNPLINK is a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets. It first removes unlikely genotypes and performs parametric and non-parametric linkage analysis in a fully automated fashion. 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
Emily Webb, Professor Richard Houlston
:: MORE INFORMATION
Webb et al. (2005)
SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.
Bioinformatics.21 (13): 3060-3061.