Downloading synonyms for dbSNP rsids
2
0
Entering edit mode
9.9 years ago
devenvyas ▴ 760

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!

dbSNP SNP • 5.5k views
ADD COMMENT
1
Entering edit mode
9.9 years ago

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

ADD COMMENT
0
Entering edit mode

The above link is expired. The RsMergeArch.bcp.gz is now available here.

ADD REPLY
1
Entering edit mode

Nope. @Pierre's link still works (late June 2018)

ADD REPLY
0
Entering edit mode

@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.

ADD REPLY
1
Entering edit mode
9.1 years ago
Mat ▴ 80

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2130 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6