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?