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NovembreLab / admixture

Repository for the admixture software
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indep-pairwise #2

Open batelz opened 1 year ago

batelz commented 1 year ago

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, --extractremoves 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 commented 1 year ago

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)