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Published September 17, 2026 | Version archive/mw_genotype_scale-pre-gatk-pin
Software Open

github.com/broadinstitute/gatk-sv/CallDeNovoSV

Authors/Creators

Description

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

Files

github.com-broadinstitute-gatk-sv-CallDeNovoSV_archive-mw_genotype_scale-pre-gatk-pin.zip

Files (19.7 kB)

Additional details

Related works

Is identical to
https://dockstore.org/aliases/workflow-versions/10.5281-zenodo.22819958 (URL)
https://dockstore.org/workflows/github.com/broadinstitute/gatk-sv/CallDeNovoSV:archive/mw_genotype_scale-pre-gatk-pin (URL)
https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fbroadinstitute%2Fgatk-sv%2FCallDeNovoSV/versions/archive/mw_genotype_scale-pre-gatk-pin/PLAIN-WDL/descriptor/RunDeNovoSVs.wdl (URL)