The R package GESE implements the gene-based segregation test described in the manuscript "Qiao, D., Lange, C., Laird, N.M., Won, S., Hersh, C.P., Morrow, J., Hobbs, B., Lutz, S.M., Ruczinski, I., Crapo, J.D., Beaty, T.H., Silverman, E.K., and Cho, M.H. (2016).  Gene-based segregation method for identifying rare variants in family-based sequencing studies.". 

The GESE pipeline demonstrates the process for applying filtering and GESE tests to the data. It also automatically generates weight matrix, if weighted GESE is needed. It assumes the data under study and the reference data are annotated using WGS Annotator. It automatically filters the study data and the reference data according to user's specification, and computes the GESE test or the weighted GESE test. This pipeline is just for demonstration purposes. More descriptions can be found in the README file.

We also provide the ExAC r0.3 SNP data annotated using WGS Annotator, which can be used as the reference data in the GESE pipeline. The data under study should be annotated using WGS Annotator v0.55, for consistent annotation.

ExAC.r0.3.annotated.snp.gz

ExAC.r0.3.annotated.snp.description.txt