CODEWITHSUNDEEP
bioinformatics
user1612753
user1612753

Reputation: 13

SNP ID conversion

Does anyone know of a way to convert single nucleotide polymorphism (SNP) IDs from rs# to SNP_A-#? I have two SNPs, rs429358 and rs4420638, and need to determine whether these SNPs are included in a different dataset. The dataset uses SNP_A-xxxxx symbols for SNP IDs. Any help would be greatly appreciated!

Upvotes: 1

Views: 2945

Answers (3)

Jeremy Jao
Jeremy Jao

Reputation: 382

The SNP_A* identifiers are Affymetrix SNP IDs. I have to do something similar too, but on a much larger scale.... Using the Affymetrix Annotation file "Genomewide SNP 6.0" from here doesn't map as much as I wanted it to: http://www.affymetrix.com/support/mas/index.affx#1_1

What I did was use Biopython (I did it in Python3). First you would have to install biopython via pip.

After you do that, you can use the Entrez library to use the esearch() method. Here is some sample code:

from Bio import Entrez

Entrez.email = '<email address>'
handle = Entrez.esearch(db='snp', retmax='1', sort='SNP_ID', term='<affymetrix id>')
results = Entrez.read(handle)
rsNumber = 'rs'+results['IdList'][0]

This should give you the correct rs number from an affymetrix id.

Upvotes: 0

Alex Stoddard
Alex Stoddard

Reputation: 8344

The SNP_A### identifiers are very likely Affymetrix SNP ids. You will need to know which array they come from but it is probably the human Genomewide SNP 6.0.

You can download annotation data from Affymetrix website which will give a rs# to affyid# mapping. Try starting at: http://www.affymetrix.com/support/mas/index.affx#1_1

Select "Annotation Files" under "Software and Data" for the Genomewide SNP 6.0 array product.

One gotcha is that some probesets on the array are redundant - for a small subset you will have multiple affyid# mapping to one rsid#

Upvotes: 1

Pierre
Pierre

Reputation: 35246

You should ask biostar: http://www.biostars.org/show/questions/

SNP_A### is not an official nomenclature. Where does it come from ?

The only way to compare your IDs would be to compare the chromosome/position/allele-ref/allele-alt.

Upvotes: 2

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