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 possible extra information. The program only accepts PLINK binary files (.bed) in order to perform the calculations as efficiently as possible.

The tests available in CASSI include those discussed by Ueki and Cordell (2012), in particular the joint effects test.

  • Includes the logistic regression epistasis test for SNP-SNP interactions, but with the possibility of adding covariates to the analysis.
  • Designed such that any number of tests may be combined to act as filters for one another, see section section 10.

CASSI is copyright, 2012-2017 Richard Howey, GNU General Public License, version 3.