Forum:Plink problem Linkage disequilibrium based SNP pruning

Question

[benhalimayossra]

Good morning everybody,

I have a problem with the LD based SNP pruning, with this command plink --file data --indep 5 1 1.25 (r² = 0.2 and the variance inflation factor is 1.25 )

The input file (ped /map) included the sample ID, population, sex, origin, and affected status I want to do SNPs selection based in their high linkage disequilibrium and to make the PCA and the DAPC.

Plink stopped working and I can't get the pruned files

[chrchang523]

What plink version are you using? What does the log look like before plink freezes?