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.
/.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