Forum: Plink problem Linkage disequilibrium based SNP pruning
0
gravatar for benhalimayossra
4.3 years ago by
Tunisia
benhalimayossra0 wrote:

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 desequilibrium and to make the PCA and the DAPC.

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

  

 

snp forum software error • 2.6k views
ADD COMMENTlink modified 4.3 years ago by chrchang5234.9k • written 4.3 years ago by benhalimayossra0
0
gravatar for chrchang523
4.3 years ago by
chrchang5234.9k
United States
chrchang5234.9k wrote:

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

ADD COMMENTlink written 4.3 years ago by chrchang5234.9k
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