-assocCC
Output case/control association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results are not generated if block type is set to ALL.
Output
TDT association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results not generated if block type is set to ALL.
Loads a set of custom tests for association.
Performs
<numtests> permutations on default association tests (or custom tests if a custom association file is specified) and writes to <inputfile>.PERMUT