BOAT (Bayesian Overlap Analysis Tool) identifies variants that are associated with two traits and tests for enrichment (i.e. whether there are more shared associated variants than expected by chance). Only summary statistics are required to implement BOAT.

Diseases often co-occur in individuals more often than expected by chance, and may be explained by shared underlying genetic etiology. When summary statistics are available, p-values are often used to assess association at a selected p-value threshold for both traits. However, p-values do not account for differences in power, whereas Bayes' factors (BFs) do, and may be approximated using summary statistics. Consequently, in overlap analyses, the use of BFs tend to result in a lower type I error rate than when p-values are used.

BOAT can be used to identify overlap variants between two traits by comparing ABFs, as well as by comparing p-values. It uses McNemar's mid-P test to assess overlap enrichment.

Download and Installation

System Requirements

The software should run on any UNIX or GNU/Linux system.

Download BOAT

Note: The current code is designed for case-control studies only.


If you have any problems running BOAT, then please contact Jennifer Asimit.


Sanger Contributors

Asimit, Jennifer

Dr Jennifer Asimit
MRC Methodology Research Fellow - Statistical Geneticist


  • A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.

    Asimit JL, Panoutsopoulou K, Wheeler E, Berndt SI, GIANT consortium et al.

    Genetic epidemiology 2015;39;8;624-34

Tool Type