Hi everyone,

I have a list of ~200k SNPs, and I'd like to generate a control set of variants with a matching MAF and LD distribution. I know that SNPsnap was built for this, but I couldn't manage to run it on my SNP list, and I think the reason is the large number of SNPs. I also tried to run SNPsnap locally, but that did not work either, as the local version still has some issues.

So, I was wondering if there is a proper alternative to SNPsnap, which can work with around 200k SNPs.

Cheers.