- HapMap, a thorough catalog of human SNPs.
- PLINK, an open-source C/C++ GWAS tool set that can analyze large data sets with hundreds of
thousands of markers genotyped for thousands of individuals to examine potential pathways.
- GRASS (Gene set Ridge regression in Association Studies), summarizes the genetic structure for each gene as eigenSNPs and uses group ridge regression to select representative eigenSNPs for each gene, assessing their association with disease risk and reducing the high dimensionality of GWAS data.
- GWAMA (Genome-Wide Association Meta-Analysis), performs meta-analysis of GWAS of dichoto- mous phenotypes or quantitative traits.