Plink, Linkage disequilibrium

[Ali Basuony]

Hello everyone,

Happy new year to all of you.

I'm using plink v.1.9 to test for linkage disequilibrium

I ran the following command

./plink --allow-extra-chr --file /stacks_out_r80p10R80maf0.05/blacklist/populations.plink --r2 --ld-window-r2 0.0 --ld-window-kb 100000 --out /stacks_out_r80p10R80maf0.05/blacklist/linkagedisequilibrium/LD.ld

# for the population.plink that is highlighted in yellow, I have populations.plink.ped and populations.plink.map in the same working directory.

And, I got these three outputs

LD.ld.ld,

LD.ld.log

and LD.ld.nosex

I think, LD.ld.ld file has all the needed information (attached are the first ten rows)

My question is, what is the next step? How I can remove the linked SNPs?

I'm using .plink.map and ped that have been generated by plink 1.9 that is implemented in the population program in stacks v2.54.

Thanks in advance for the help.

Ali

[Christopher Chang]

As a practical matter, you probably want to use --indep-pairwise (followed by --extract/--exclude on one of its output files) to perform LD pruning.  While it's possible to use the output of --r2 for this purpose, that would take substantially more work.

[Ali Basuony]

Thanks so much for the help. It works fine.

Ali