I am working with an old dataset containing gwas summary stats without positions. As part of my project I need to LD-clump the summary stats and estimate an LD matrix of selected variants. To do this I need a reference genome, which I am using the 1000 Genomes dataset for.
The problem however is that many of the lead SNPs in my dataset does not exist in the reference set. The reason for this is that some SNPs have been assigned to new RsID's due to various reasons. The problem I am facing is that some of the SNPs that exist in my dataset exist under a different name in my reference dataset. How do I update outdated RsID's in a GWAS summary result where base pair position is not available?