What Omni genotype data do you have?

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/

Related questions: