BGEN
A reference implementation of the BGEN format, written in C++.
QCTOOL
The QCTOOL program for manipulation and quality control of genome-wide datasets.
HPTEST
Software to test for genetic association between hosts and pathogens. HPTEST is built with QCTOOL.
LDBIRD
Software to compute and histogram pairwise LD metrics. LDBIRD is built with QCTOOL.
BINGWA
Software for bayesian and frequentist meta-analysis of genetic association test summary statistics.
OpenSNPTEST
Under development - watch this space...