BiForce looks very promising – great find!

I’m sure detecting relevant epistasis is going to be the name of the game pretty soon. Very few “interesting” traits are not complex!

”
Gene-gene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS.”

“We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (case-control) traits. BiForce achieves great computational efficiency by using memory efficient data structures”

So, perhaps tools such as the above can help resolve the problem of epistasis.