SNPLINK: Multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.
Webb et al. have developed the program SNPLINK to undertake full genomewide linkage analysis in an automated fashion. Since linkage disequilibrium between densely spaced SNP markers can inflate linkage statistics, SNPLINK performs automated linkage disequilibrium removal and then re-calculates linkage statistics.
Example files can be copied from /usr/local/snplink/.
The postscript output plots can be viewed with Ghostscript (gs, see below). This requires an Xwindows connection to Helix. Alternatively, the plots can be transferred to your desktop machine and viewed with any local postscript displaying software.
% cd /home/user/run1 # THis directory contain example files % perl /usr/local/snplink/snplink.pl example1.in Parameters read Carrying out nonparametric analysis.... Chromosome 1 complete Initial scan and error removal complete Chromosome 1 LD measures computed LD measures computed LD removed using Dprime measure Plotting graphs..... LD removed using rsq measure Plotting graphs..... %
% gs /home/user/run1/rsqLDexample/Rplots.ps
Word doc: snplink