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