HapMap

Description

The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals.

Datasets

From http://www.hapmap.org/downloads/index.html.en

The following directories contain HapMap project related data, software, and documentation, that have been made publicly available. (See [HTML_REMOVED] HapMap Data Access Policy[HTML_REMOVED] for more information). More details about each dataset can be found in READMEs in the respective directories:

  • Bulk data 

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  • Genotypes: Individual genotype data submitted to the DCC to date. 

    • \\xfc\\xfdli\\xfd\\xfc\\xfc\\xfda href="http://www.hapmap.org/downloads/ld_data/?N=D" target="_blank" rel="nofollow"\\xfd\\xfcLD Data\\xfc\\xfd/a\\xfd\\xfc: Linkage disequilibrium properties D', LOD , R<sup>2</sup> compiled from the genotype data to date\\xfc\\xfd/li\\xfd\\xfc

  • Phasing Data: Phasing data generated using the PHASE software, compiled from the genotype data to date.

  • Allocated SNPs: dbSNP reference SNP clusters that have been picked and prioritized for genotyping according to several criteria (see info on how SNPs were selected). The file 00README contains per-chromosome SNP counts and further details.
  • Frequencies: Allele & genotype frequencies compiled from genotyping data submitted to the DCC to date. These have also been submitted to dbSNP and should be available in the next dbSNP build.

    •   \\xfc\\xfdli\\xfd\\xfc\\xfc\\xfdb\\xfd\\xfc\\xfc\\xfda href="http://www.hapmap.org/downloads/recombination/latest/" target="_blank" rel="nofollow"\\xfd\\xfcRecombination rates and Hotspots\\xfc\\xfd/a\\xfd\\xfc\\xfc\\xfd/b\\xfd\\xfc: Recombination rates and hotspots compiled from the genotyping data.

  • SNP assays: Details about assays submitted to the DCC to date. PCR primers, extension probes etc., specific to each genotyping platform.
  • Perlegen amplicons: Details for mapping Perlegen amplicons to HapMap assayLSID. For primer sequences, see Perlegen's Long Range PCR Amplicon data.
  • Raw data: Raw signal intensity data from HapMap genotypes. Currently includes data from Affymetrix GeneChip 100k and 500k Mapping Arrays.
  • Inferred genotypes: Genotypes inferred using the method of Burdick et al. Nat Genet 38:1002-4
    • .

    Openness: OPEN

    Additional Information

    Field Value
    Source http://www.hapmap.org/
    Author Author not given
    Maintainer Maintainer not given