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.
Thanks!
Do you have a table of merged SNPs somewhere within dbSNP?
http://www.ncbi.nlm.nih.gov/books/NBK44395/#FTP.do_you_have_a_table_of_merged_snps_s
The rs merge table (RsMergeArch) is on the dbSNP ftp site, and the column definitions for it are located in dbSNP_main_table.sql.gz, which can be found in the shared_schema directory of the dbSNP FTP site. The rsHigh column in the RsMergeArch table contains the rsID numbers that merged away (rsHigh is merged to rsLow). Due to multiple merge events, sometimes rsLow is merged even further. The "rsCurrent" column refers to the current refSNP. (11/14/07)"
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz
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Pierre Lindenbaum
The above link is expired. The RsMergeArch.bcp.gz is now available here.
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janhuang.cn
@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_data and is alive.
You can download a list of "main" rsIds and their synonyms according to the latest Ensembl version here: http://genehopper.ifis.cs.tu-bs.de/downloads
Hope, this helps.
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