Published August 19, 2024
| Version v0.29-beta
Software
Open
broadinstitute/gatk-sv: v0.29-beta
Creators
- 1. Broad Institute
- 2. Fulcrum Genomics
- 3. Dana-Farber Cancer Institute
- 4. @broadinstitute
- 5. @LokaHQ
- 6. @populationgenomics
- 7. @UMCCR
Description
What's Changed
Critical
This release includes a critical bug fix to the SplitVariants task in GenotypeBatch. The affected workflow was GenotypeBatch, and the affected version was v0.28.5-beta. We recommend immediately updating to v0.29-beta. If you ran GenotypeBatch with v0.28.5-beta, please check if any records were dropped. If in doubt, re-run with v0.29-beta. More details in #712
Pipeline functionality updates
- Integrate ReshardVcf into ResolveComplexVariants
- Remove CHR2 and END2 from INS in CleanVcf
- Fix --par arg to compute_AFs.py in ShardedAnnotateVcf
- Updates to allele frequency annotation fields
- Grouped MEIs with insertions in splitvariants.py
Performance improvements
- Reimplement ParseGenotypes in GenotypeComplexVariants
- Reduce memory usage in GenotypeSRPart1
- Set the default disk size in AnnotateIntervals as a function of input files size
- Making the Vapor plots optional to store as a final output
- Make per-sample QC plots optional in MainVcfQc
Fixing bugs and small annoyances
- Skip subsampling if batch size is less than n_samples_subsample
- Add NonZeroReferenceLengthAlignmentReadFilter read filter to CollectSVEvidence
- Prevent sample ID mangling in WGD computation
- Update gatk docker with changes to handle CPX_TYPE for CTX
- Fix UnboundLocalError in EvidenceQc
- Update gnomad-v2 sample-level benchmarking data path
Documentation
- Terra dashboard updates
- Reorganize docs on running the pipeline
- Add CONTRIBUTING.md
- Update Docusaurus and its dependencies to v3.3.2
- Update docs on building and hosting Docker images
- Update docs on building inputs
- Add documentation for rename_samples in GatherBatchEvidence
CI/CD, workflow organization, and auxiliary scripts
- Deprecate single-batch Terra configs
- Add support for incomplete workflows in get_inputs_outputs.py
- Trigger WDL tests on changes to /inputs and fix Terra config tests
- Update deprecated Pandas append operation for monitoring log analysis
- Extend the list supported syntax-highlighting languages
Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.5-beta...v0.29-beta
Files
broadinstitute/gatk-sv-v0.29-beta.zip
Files
(22.4 MB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/broadinstitute/gatk-sv/tree/v0.29-beta (URL)