Genomic Association Tester (GAT)

Welcome to the home page of the Genomic Association Tester (GAT).


A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, in the interpretation of ChIP-Seq or RNA-Seq data. Because of complex genome organization, its answer is non-trivial.

The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation and can take into account genome organization like isochores and correct for regions of low mapability.

GAT accepts as input standard genomic file formats and can be used in large scale analyses, comparing the association of multiple sets of genomic intervals simultaneously. Multiple testing is controlled using the false discovery rate.

In this manual, the Introduction covers the basic concepts of GAT. In order to get an idea of typical use cases, see the Tutorials section. The Usage instructions section contains a complete usage reference.

Developers’ notes

The following section contains notes for developers.

Indices and tables