indep-pairwise

[batelz]

Hi,
I'm trying to set a bed file with non-LD SNPs in order to run ADMIXTURE.
according to your manual, it is revised to run --indep-pairwise, following by removal of the LD SNPs.

the --indep-pairwise yields two lists:
pruned.in - SNPs in LD
pruned.out - SNPs not in LD.

then, for the removal of the SNPs:
plink --bfile rawData --extract plink.prune.in --make-bed --out prunedData
according to the plink manual,
--extract removes all the variants that are missing = keeps SNPs in prune.in.

The way I understand it - this command will keep the SNPs that are indeed in LD.

Did I miss anything?

[npsonis]

One colleague of mine just pointed this out:
According to the manual
pruned.in produce a pruned subset of markers that are in approximate linkage equilibrium not disequilibrium (LE no LD) with each other (the snps that you want to keep or extract)