What types of genotyping data do you have?

The 1000 genomes project has multiple sets of high density genotype information on both Illumina and Affymetrix Platforms.

Affy 6.0 genotype

Coriel has carried out Affy 6.0 genotyping on many of the samples which are part of the NHGRI Cell line catalog.

These files are available on our FTP site in release/20130502/supporting/hd_genotype_chip/

Axiom genotype

The Affymetrix Axiom Exome chip was used to genotype some samples for the phase 1 analysis. There are genotypes for 1248 1000 Genomes samples from the Affy 6 chip available in phase1/analysis_results/supporting/axiom_genotypes from the Axiom Exome Chip

Omni genotype

Both the Sanger Institute and the Broad Institute have carried on genotyping of 1000 Genomes and HapMap samples on the Omni Platform. The most recent set of Omni genotypes can be found in the phase 3 release directory release/20130502/supporting/hd_genotype_chip/ These contain GRCh37 based vcf files for the chip, and normalised and raw intensity files.

The ShapeIt2 scaffolds for these data, which were used in the phase 3 haplotype refinement project, can also be found in the phase 3 supporting directory release/20130502/supporting/shapeit2_scaffolds/.

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