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.
/carrot: Carrot tests/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 dockers, 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
This repository is maintained following the norms of
continuous integration (CI) and continuous delivery (CD).
GATK-SV CI/CD is developed as a set of Github Actions
workflows that are available under the .github/workflows
directory. Please refer to the workflow's README
for their current coverage and setup.