Bioconductor: an open source software for bioinformatics which provides tools for the analysis and comprehension of high-throughput genomic data using the R statistical programming language.
PLINK: a free, open-source whole genome association analysis toolset focusing on analysis of genotype/phenotype data.
PLINK/SEQ: an open-source C/C++ library providing a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies.
METAL: a tool for meta-analysis of genomewide association scans by combining test statistics and standard errors or p-values across multiple studies.
MAGENTA: a computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes.
IMPUTE2: a genotype imputation and haplotype phasing program