Updating old RsID's to new RsID's

Question

[f-rasmussen]

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 How do I update outdated RsID's in a GWAS summary result where base pair position is not available?

[mauribrunner]

Hi f-rasmussen. Could you give me an example of an rs that has been modified? What versions of dbSNP are you working with?

Answer 1

[Sophia]

The "rsnps" package (an R programming language package) is very helpful for conversion (and gives other details on SNPs in addition to their most up-to-date rsID): https://cran.r-project.org/web/packages/rsnps/rsnps.pdf

The function ncbi_snp_query() would likely be the one you want to use for this action. Just read in your table to R and execute this function (see linked documentation for package installation instructions and more details on this function).