1 Introduction

CASSI (Contrived Acronym of Software for SNP Interactions) is a C++ program written to analyse SNP-SNP interactions, analysing a choice of SNPs from two given SNP windows (possibly from different pedigree files). Each pair of SNPs whose interaction test passes a given significance level is returned in the output file with extra information for the performed test. The program only accepts PLINK binary files (.bed) in order to perform the calculations as efficiently as possible.

The only test that is currently available is the joint effects test Ueki and Cordell (2012), details of this test are given in section 4. Further interaction tests are planned for CASSI so watch this space!

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