Core set of 1KG SNPs

For several of our analyses, we have defined a "core" set of 1KG SNPs to interrogate. We are hosting this file here for download, along with a brief description of how we generated the set.

To make the file, we:

  1. Started with all 1KG SNPs
  2. Removed all SNPs with a MAF < 5%
  3. Removed all SNPs within 50bp of another SNP
  4. Removed all SNPs in regions with known mappability issues[1]
This final SNP set has 4,828,763 SNPs, and has the following fields: 1-3) bed-style coordinate, 4) rsID, and 5) global allele frequency.

Click here to download the file (~58M)

[1] Degner et al, 2009