How To Calculate All Ld Results For 1000G Raw Genotypes?

Question

[J.F.Jiang]

Hi everyone,

I am using the raw 1000G genotypes 20101123 release version to calculate all the LD results for paired SNPs.

Last time if I want to look at the proxy SNPs that are in LD with the specific SNPs, I will use the --ld-snp-list option in PLINK.

As offered by PLINK, if I want to calculate all LD results, in which the r2>=0.5, I should use plink --bfile mydata --r2 --ld-window-r2 0.5

But after the calculation, I find it maybe not the right results because I only get a result of 1.4G for CEU population, and further more when I search the result with my last snp-list file, I find much fewer results.

So based on my question, there must be an important thing I miss.

Could any one can give some suggestions?

Answer 1

[inesdesantiago]

Hello. I am looking for the same kind of thing. Did you find a solution? I have 1000G genotypes data. I also have a list of 54 SNPs and I would like to get all LD pairwise SNPs with each one of my 54 SNPs.. Any ideas on how to do this? I have never use Plink... should I try "plink --bfile mydata --r2 --ld-window-r2 0.5 "?

[J.F.Jiang]

that's will be much easy for a list of SNP, try to find in the documentation in PLINK

plink --bfile --r2 --ld-window-r2 --ld-snp-list --ld-window