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Calculating number of SNPs in linkage disequilibrium at different thresholds from 1000 genomes project using PLINK

I want to calculate the total number of SNPs in linkage disequilibrium at various thresholds (r2 > 0.1, 0.2, 0,3 etc) using PLINK as described in this paper (doi: 10.1093/bioinformatics/btu655).

How can I do this for all SNPs in the 1000 genomes project? My main goal is to create a 'control' set of SNPs (using SNPs in the 1000 genomes project) with a similar LD structure as my SNPs of interest.

Thanks in advance and sorry if I am misusing terminology, I am not particularly familiar with these sorts of analyses.

plink linkage snp ld disequilibrium
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updated by Ram Ram • written by octopuslegs11 • octopuslegs11

Do you want to do it for every single SNP? This will take a long time. Theoretically you could calculate the LD between every pair of SNPs and then get a huge matrix.

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written by DBScan • DBScan

I was hoping so.

Alternatively, could I just use the LD score and only use SNPs in the 1000 genomes project with a similar LD score to my SNPs of interest?

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written by octopuslegs11 • octopuslegs11

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