The 1000 genomes project has genotype data from two different high density genotyping platforms.

The Illumina Omni Platform

Both Illumina and the Broad institute have carried on genotyping of 1000 genomes and Hapmap samples on the Omni Platform. The set run at Illumina can be found in 20101206_hapmap_omni_results and the set run at the Broad Institute can be found at 20111117_omni_genotypes_and_intensities . Both sets have files in NCBI36 and GRCh37 coordinates. The individuals in these two sets overlap but are non identical. Where an individual is found in both files it represents a technical replicate carried out by both centres. The set of snps between the two data sets is not identical. Neither snp set was filtered so any missing snp from one file failed to perform on the given samples in the file. These snps should all have a Genetrain or GeneCall score associated with them. While internally project specific clustering will determine exactly what cut off to use when discarding sites with low genetrain or genecall scores as a rough guide a score of 0.15 or greater is a reasonable cut off.

The Affymetrix Axiom Platform

There are Affymetrix Axiomgenotypes available for 1261 Hapmap 3 individuals some of whom are also part of the 1000 genomes. The snps reported in this file are mapped to GRCh37 and are unfiltered. As some of the individuals were screened on earlier versions of the Axiom platform some of the genotype data is missing. For more details on this data set please read the README