sixpac

SIXPAC is an efficient, scalable search algorithm that finds synergy between multiple loci (genome-wide) in large case-control datasets.

In its present avatar, SIXPAC tests each pair of SNPs for 4 joint-effect models (dom-dom, dom-rec, rec-dom, rec-rec) and outputs statistically significant synergistic effects that predispose an individual to disease. It takes genotype and phenotype information as input, encoded in "raw" and "map" file formats - as defined by Shaun Purcell’s Plink software. It outputs a list of interacting alleles whose combinations are significantly enriched in cases relative to controls (or vice versa).

SIXPAC is fast: genome wide scans of large datasets (thousands of samples, typed at ~1M SNPs) can be processed overnight.