Sample Cel File Dataset For Affymetrix Axiom Genotyping Platform

Question

[pufferfish]

I'm looking for a dataset that can be used to test students' ability to do genotype calling using the Affymetrix Power Tools pipeline.

As such, it should ideally:

• come with known genotypes
• contain more than one ancestral group (for testing ability to find structure etc)
• not be too well known,

..although none of theses are dealbreakers

I've tried:

• the Affy website: only seems to have called genotypes
• The Broad Institute website
• 1000 genomes data server

None of these resources seem to make this sort of dataset available, although they must have them internally. Any advice?

EDIT: To be clear, I'm looking for Axiom data, not SNP6

Answer 1

[Matt Shirley]

You'll find plenty of Affy 6.0 CEL files on the HapMap FTP site. You'll also find genotypes on the same site as well. This file maps the naming scheme to HapMap NA accessions. You'll also be able to determine the ancestral groups from this file.

[pufferfish]

Thanks, but I'm looking for Axiom data. Mentioned in the title and have now added to the question text

[Matt Shirley]

Sorry, I didn't catch that. It seems that Affymetrix does supply 90 Axiom Exome319 CEL files for the HapMap YRI population.

Answer 2

[Peixe]

Have you tried the GEO Datasets? Don't know much about it, but i remember once I did a similar exercise with it...

[pufferfish]

Didn't occur to me to check GEO. Doesn't seem to have any Axiom datasets though

Answer 3

[Neilfws]

Start from the GEO platforms page and search for the SNP array platform of interest. For example "affymetrix snp 6.0".

That query currently returns 3 platforms. One of these is GPL6801. This links to 178 datasets (GEO series) and 10 735 samples. Many of those series have supplementary CEL file data available.

[pufferfish]

That data is SNP6, not Axiom