Is there a good way to take any two SNPs and pull out the LD between them, particularly the R-squared and the directionality of the linkage (e.g. A in SNP1 occurs with G in SNP2 95% of the time)?
Obviously I can do this manually, but I am wanting to do it for a list of several thousand SNPs, so I am hoping for a scalable solution. Right now I can't find anything, and it looks like I will have to come up with my own solution using
vcftools and the 1000 genomes data.