I am using GWAS data (with plenty of missing cells) which inconsistently lists SNPS with the rs ID or chromosome ID. Is there an automated method to convert from Chr ID to the SNP rs #?
If you have it in ped/bed format you can use plink for it. I routinely use update names option together with --range to match variants by the their physical position, and then filter only those with new names by using --keep flag