Question: How to convert Affymetrix SNP IDs to dbSNP rs SNP names
gravatar for philipovic
5.0 years ago by
philipovic10 wrote:

For my project I would like to convert the Affymetrix SNP IDs to dbSNP ID's, using a Affymetrix Axiom array.

To convert the SNPs (called "AX-{number}"), I used the annotation file which works for most SNPs, however for some Affymetrix IDs there is no rs number dbSNP ID available.

For example, my file is coded as:
1       AX-13216142     0.0009  86028   C       T

where column 2 is the SNP name, in my annotation file the corresponding RS number is given (rs114608975) however, not for every SNP

Could someone explain why this is and how to get the right rs number out of these SNPs?

Thank you!

affymetrix plink snp genome • 3.6k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by philipovic10

If you want to track SNP by its position you also would need to know which hg reference genome to look at. You might convert your plink files to VCF (with plink). Then look in the header at chromosome lengths and see if they match any chromosome lengths in NCBI or UCSC hg reference versions (or if you are lucky, vcf file will contain hg version as well). But I am pretty sure you will not be able to match those lengths (microarray / ngs difference).

I had the same problem with affymetrix SNP IDs, in the end you must write to the company and ask for full annotation file. I haven't got any response, so I just gave up annotating those SNPs.

Also be aware to strand flipping. Microarrys don't say if it's + or -. There should be information in annotation file, but I think it's better to grab UCSC annotation for let's say hg19, look up by SNP rs and make all SNPs on the same strand. It doesn't matter if you are working only with this file, but does make a lot of problems when trying to add data from outside

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by stolarek.ir650
Could you post an example?
ADD REPLYlink written 5.0 years ago by cpad011214k

Yes, I edited my post

ADD REPLYlink written 5.0 years ago by philipovic10

Thanks for the update. If 86028 is the position in above example, check if you can grab chr number as well. Could you please post the chip details you are using? I guess page 62 (of 90) in manual will help you to print chromosome columns (assuming that you are using Affymetrix Axiom Genome-Wide chip).

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by cpad011214k
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