Published June 27, 2023
| Version v0.28-beta
Software
Open
broadinstitute/gatk-sv: v0.28-beta
Creators
- 1. Broad Institute
- 2. Fulcrum Genomics
- 3. @broadinstitute
- 4. Dana-Farber Cancer Institute
- 5. @LokaHQ
- 6. @populationgenomics
- 7. @UMCCR
- 8. MGH
Description
What's changed
Improvements to SR genotyping and INS breakpoints:
- Update SR counting and genotyping
Filtering workflows:
- Update ApplyManualVariantFilter json template
- Update VaPoR workflows
- SVConcordance workflows update
- Fix CTX END2 error in GATK formatting script
Other workflows:
- Fix non-deterministic errors in GetSampleIdsFromVcfTar
- make the RunMELT task a little more robust
- Improve STR workflow
- Remove DeleteIntermediateFiles task
- Remove unused ped_file input from GenotypeBatch and RegenotypeCNVs
Docker build:
- Manually install MASS R package in sv-pipeline-virtual-env
- Build and publish images to multiple registries in one job, & update the dependencies of the action
Other scripts, docs, and JSONs:
- Update copy_outputs.py
- Generate Terra workspace tsv files from transposed tables
- Update README to link to SV callers used
- Remove ped file from workspace data TSV for cohort mode terra workspace
Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.27.3-beta...v0.28-beta
Files
broadinstitute/gatk-sv-v0.28-beta.zip
Files
(22.3 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/broadinstitute/gatk-sv/tree/v0.28-beta (URL)