The Genome-Wide SNP 5.0 Sample Data Set is a useful tool for software and workflow demonstrations, development of probe-level analysis methods for making genotype calls from probe intensity data, and for a variety of other applications.

The data set consists of 10 trios comprised of 30 distinct HapMap CEPH samples, including some replicates: Four samples are replicated four times, and one sample is replicated three times.

The HapMap Project has made available a large number of reference genotypes which can be used in conjunction with this data set. The HapMap data access policy limits redistribution rights on these genotypes so they cannot be made available directly by Affymetrix, but the reference data can be downloaded from the HapMap Project. As of HapMap release 21a, a total of about 485,509 SNPs have reference genotypes available for the samples shared here. These numbers are steadily increasing with each HapMap update.

The data set has been split into five parts for convenient download. The data consists of GeneChip® Operating Software (GCOS) CEL and XML files as well as Affymetrix GeneChip® Command Console™ Software (AGCC) CEL, CHP and ARR files. AGCC will be the replacement for GCOS (http://www.affymetrix.com/products/software/specific/command_console_software.affx). The README file contains additional information about these samples.The available options for download are: