I know that sometimes identical SNPs get given two different numbers and later on someone corrects that. I have an old list of dbSNP rsids from an old Illumina chip from circa 2008, and I have two sets of non-standard VCFs from about 2012 and 2013 that have rsids built-in.
I logically conjecture that there may be cases where a SNP is present in both the list and the VCFs but by different names. I have a script that UF HPC awesomely wrote for me that filters the VCFs based on any list of rsids I give it. SNPs that are being referred to by two (or three) names may be unfortunately lost.
I was wondering, how can I download a list of all the synonyms of all the rsids in my list? That way I can include the synonyms in my list, and thus only miss sites for which there is no data.
The above link is expired. The RsMergeArch.bcp.gz is now available here.
Nope. @Pierre's link still works (late June 2018)
@Janhuang: URL posted in your post has an extra "data" string after database. URL should be:
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_dataand is alive.