Converting list of Affy SNP ids to dbSNP rs ids

Question

[devenvyas]

There is a data set that I want to work with (ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/) to do some PCA analyses (see New to SNP data: I need help getting Affy Axiom data out of genotyping console into a Principle Component Analysis)

Anyways, I've downloaded the data set, but I have come to learn that the annotation file (ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/annotation.txt) and the map/ped files (ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/all_snp.ped.gz, ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/all_snp.map.gz) I need refer to the Affy SNP ids, not the dbSNP rs ids.

How can I convert the ids en masse to dbSNP rs ids?

[devenvyas]

Can anyone suggest a script that could help me do this? Thanks!

[josmell.sevillano.o]

I have the same problem, anyone have a script to help us? Please. Thanks!

[josmell.sevillano.o]

I got the answer, check the link: https://stackoverflow.com/questions/7846476/replace-column-in-one-file-with-column-from-another-using-awk

Answer 1

[dandan]

Affymetrix supplies this information (Affymetrix IDs to rs ids) on their website. First find the Affymetrix chip that was used to create the dataset, then look it up on www.affymetrix.com. Go to the "Technical Documentation" tab and then scroll down till you find the annotation files (for example, for this chip, you go to the "Current NetAffx Annotation Files" area). Download the CSV with all the annotations. The first column is the Affymetrix ID, the second column is the corresponding rs ID. You can write a script to convert these en masse.

For example, the Affymetrix 6.0 chip data is available at http://www.affymetrix.com/catalog/131533/AFFY/Genome-Wide+Human+SNP+Array+6.0#1_3.

Hope that helps. Good luck!

[devenvyas]

I knew those files exist, but I don't know what to do with them (i.e., I don't know enough Python/Perl to write one from scratch). Could you point me to a template script that I could adapt to my needs? Thanks!