I wish to perform a random permutation analysis, for which I need to randomly select SNPs. I was thinking that these SNPs should ideally come from a list of all independent SNPs. Initially I thought that I could perform clumping or pruning of e.g. HapMap data in PLINK, but upon closer inspection I'm not sure this would work, as both have some kind of selection (MAF or P-value) that might introduce a bias in my independent SNP set. Not to mention the fact that I don't actually have p-values to base this on.
This random permutation analysis I'm attempting isn't new, so I'm wondering if there are existing SNP datasets of independent SNPs I could use. Or how I could best go about creating my own.
Any help is appreciated!