Athena is a command-line toolkit written in python to facilitate the modeling of SV mutation rates and dosage sensitivity. Athena is under active development, but a reasonably stable alpha version is available on GitHub. Read more about Athena
CNView is an open-source tool written in R for visualization and annotation of copy-number variation from whole-genome sequencing data. The CNView codebase and documentation are available from GitHub, and a description of the method is provided in our preprint manuscript, Collins et al. (2016).
GATK-SV is a structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data. It is designed for use on cohorts (>100 samples), although it also supports a single-sample mode. Ryan co-led the development of the alpha version of GATK-SV, and used it to produce the gnomAD-SV reference catalog as described in Collins*, Brand*, et al., Nature (2020). GATK-SV is available... Read more about GATK-SV