Here's a list of software you may be interested in:
QCTOOLis a program for manipulation of genetic datasets.
bingwaimplements frequentist and bayesian meta-analysis based on association test statistics
inthinneratorcan be used for a variety of tasks to do with "thinning" genetic data - e.g. generating association regions with picked 'lead SNPs' in a GWAS scan, or thinning data for use in principal components analysis.