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Genie is a general-purpose tool to analyze association and transmission disequilibrium (TDT) between genetic markers and traits in studies of families and independent individuals. It implements 3 analysis options. PedGenie for performing genetic association analysis in studies of families of arbitury sizes and structure, and independent cases and controls. hapMC for performing analysis on haplotype data. It uses Monte Carlo procedure and Expectation-Maximization estimates of haplotypes to provide valid haplotype tests for various standard association statistics. hapConstructor for exploring multi-locus associations in candidate genes and regions. It automatically builds multi-locus SNP sets to test for association in a case-control framework.

What’s new in


PedGenie Descritpion and Functionality


hapMC Description and Information


hapConstructor Description and Information


Java runtime, Genie.jar, .rgen parameter file and pedigree file(s)optional files : allele or haplotype frequency file; quantitative data file and linkage parameter file

How to execute

java -jar Genie.jar analysis_option rgenfile[.rgen]

Output Report

Output Report written to[.rgen file name].report or [.rgen file name].summary file.

.rgen Parameter File

Detailed description of .rgen XML file

Example Files

All PedGenie, hapMC, hapConstructor and QTDT example files

QTDT Interface

PedGenie / QTDT Interface Package


Download Genie and QTDT Interface packages

To Reference Genie

Reference information


Please send name and email address to Steven Backus

Last update : 28 Aug 2020Publications    References    Bugs    FAQ    Disclaimer    Contact/Requests