piMASS (Posterior inference using Model Averaging and Subset Selection) performs multi-SNP association with disease phenotypes. It can handle all SNPs in the genome simultaneously.piMASS was developed to perform multi-SNP association analysis for large (genome-wide) datasets, although it can also be applied to smaller association analysis data (e.g. candidate genes or regions), and in this case it forms an alternative to the multi-SNP association analysis capabilities of BIMBAM (below). It may also be useful for Bayesian variable selection regression in large-scale problems more generally.
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Ann. Appl. Stat. Volume 5, Number 3 (2011), 1780-1815.
Bayesian variable selection regression for genome-wide association studies and other large-scale problems
Yongtao Guan and Matthew Stephens