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Convert #Ss To #Rs Snp Ids

Hi

I have about 500k #ss SNPs (from an Affy 5.0 chip). I would like to find the #rs numbers for each of these SNPs. Would anyone happen to know how would I go about doing this? I also have allele names for each #ss number, but no physical or genetic positions.

Thanks very much!

snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by explodecomputer • explodecomputer

1 answer

A table linking the #ss to the #rs is available at ncbi at : ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/SNPSubSNPLink.bcp.gz

CREATE TABLE [SNPSubSNPLink]
(
[subsnp_id] [int] NULL ,
[snp_id] [int] NULL ,
[substrand_reversed_flag] [tinyint] NULL ,
[create_time] [datetime] NULL ,
[last_updated_time] [datetime] NULL ,
[build_id] [int] NULL ,
[comment] [varchar](255) NULL
)
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written by Pierre Lindenbaum Pierre Lindenbaum

Sorry for my slow response to your very quick one. Many thanks for this info!

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written by explodecomputer • explodecomputer

sir.. is there any method available to convert #rs to#ss id??

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written by keerthuguna96 • keerthuguna96

Hi Pierre, I am interested to know how you open this large bcp file. Which software you use to process or how should I do it. That file is huge 150 GB after decompress. It will really help me if you give some insight on this.

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written by mrkmm • mrkmm

what do you mean with 'open' ? this is a tab delimited file that any linux tool can process on the fly.

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written by Pierre Lindenbaum Pierre Lindenbaum

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