I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from here. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele, Non_Effect_allele, Beta, SE, Pvalue.
My ultimate aim is to identify SNPs in the tagging set that are in LD with each of index SNPs. I need to calculate r2 between index SNPs and tagging SNPs within 1MB window and get a table of index vs tagging SNPs (r2>0.8).
How can I use PLINK to carry out this work? I'm new to PLINK and LD clumping