Genomic Exhaustive Collapsing Scan (GECS)

GECS is an implementation of a novel approach to conduct exhaustive region-based association analysis of rare variants in genomic case-control studies.

An exhaustive genomic scan for association

The main idea of the exhaustive scan is to compute test statistics for all contiguous subsequences of larger sequences, such as human chromosomes. The idea of the exhaustive one-dimensional scan can be regarded as analogous to Kulldorff's two-dimensional spatial scan (Kulldorff, 1996).

GECS is written in C++ and implements an ultrafast algorithm that enables testing for association of all genomic subsequences using the collapsing test of Li and Leal (2008). The application is highly scalable and suitable for running analyses on large whole-exome and whole-genome studies.

GitHub Repository: https://github.com/ddrichel/GECS