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Sample Cel File Dataset For Affymetrix Axiom Genotyping Platform

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

affymetrix
• 7,183 views • link
written by pufferfish pufferfish

3 answers

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.

• 137 views • link
written by Matt Shirley Matt Shirley

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

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written by pufferfish pufferfish

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

• 158 views • link
written by Peixe Peixe

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

• 0 views • link
written by pufferfish pufferfish

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.

• 0 views • link
written by Neilfws Neilfws

That data is SNP6, not Axiom

• 0 views • link
written by pufferfish pufferfish

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