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:
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.
- Started with all 1KG SNPs
- Removed all SNPs with a MAF < 5%
- Removed all SNPs within 50bp of another SNP
- Removed all SNPs in regions with known mappability issues
Click here to download the file (~58M)
 Degner et al, 2009