GATK-SV A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data. For technical documentation on GATK-SV, including how to run the pipeline, please refer to our website. Repository structure /.github: Continuous integration (CI) and continuous delivery (CD) workflows /dockerfiles: Resources for building pipeline Docker images /inputs: Files for generating workflow inputs /templates: Input JSON file templates /values: Input values used to populate templates /scripts: Scripts for running tests, building Docker, and analyzing Cromwell metadata files /src: Main pipeline scripts /RdTest: Scripts for depth testing /sv-pipeline: Various scripts and packages used throughout the pipeline /svqc: Python module for checking that pipeline metrics fall within acceptable limits /svtest: Python module for generating various summary metrics from module outputs /svtk: Python module of tools for SV-related datafile parsing and analysis /WGD: Whole-genome dosage score scripts /wdl: WDLs running the pipeline. There is a master WDL for running each module, e.g., ClusterBatch.wdl. /website: Website code