Note that this document relates to the interim release of genotyping data on 150K participants in 2015 and has been superceded.

This guide provides information and instructions for analyzing Axiom genotyping array data. It includes the use of Affymetrix Genotyping Console Software (GTC) or Affymetrix Power Tools (APT) and SNPolisher R package to perform quality control analysis (QC), for samples, plates, and SNP filtering prior to downstream analysis, and advanced genotyping methods. While this guide contains specific information tailored to analyzing Axiom genotyping array data, most principles can be applied to all Affymetrix genotyping array data with the QC metrics being array specific (e.g., contrast QC for Genome-Wide SNP 6.0 Arrays vs. dish QC for Axiom arrays).

The document was last updated in 2014.

This resource can be downloaded or viewed using the link: axiom_geno_analguide.pdf

If you have wget available (typically on linux systems), then you can also obtain a copy using the command

 wget  -nd  biobank.ctsu.ox.ac.uk/ukb/ukb/docs/axiom_geno_analguide.pdf