https://github.com/broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
https://github.com/broadinstitute/gatk-sv
bioinformatics genomics structural-variants structural-variation
Last synced: 6 months ago
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A structural variation pipeline for short-read sequencing
- Host: GitHub
- URL: https://github.com/broadinstitute/gatk-sv
- Owner: broadinstitute
- License: bsd-3-clause
- Created: 2020-06-18T20:52:07.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2025-04-10T16:27:17.000Z (7 months ago)
- Last Synced: 2025-04-10T18:04:18.795Z (7 months ago)
- Topics: bioinformatics, genomics, structural-variants, structural-variation
- Language: Python
- Homepage: https://broadinstitute.github.io/gatk-sv/
- Size: 84.3 MB
- Stars: 186
- Watchers: 13
- Forks: 75
- Open Issues: 104
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.TXT
- Code of conduct: CODE_OF_CONDUCT.md
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README
# 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](https://broadinstitute.github.io/gatk-sv/).
## Repository structure
* `/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
## CI/CD
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](.github/workflows/README.md)
for their current coverage and setup.