Published May 2, 2024
| Version v0.28.5-beta
Software
Open
broadinstitute/gatk-sv: v0.28.5-beta
Creators
- 1. Broad Institute
- 2. Fulcrum Genomics
- 3. Dana-Farber Cancer Institute
- 4. @broadinstitute
- 5. @LokaHQ
- 6. @populationgenomics
- 7. @UMCCR
- 8. MGH
Description
Updates
GatherSampleEvidence
- Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES
- Make LocalizeReads optional
- Make manta region bed index required
- Make MELT scripts independent of the execution path
Main pipeline
- Rewrite SplitVariants in TasksGenotypeBatch.wdl
- Disable MakeCohortVcfMetrics by default
- Find CN field for mCNVs in MainVcfQc without hard-coding order of format fields
- Update BEDTools version to 2.31.0
- Two small bugfixes to EvidenceQc
- Update gatk_docker with CPX annotation changes to SVAnnotate
- Reduce redundant docker image inputs:
sv_pipeline_base_docker
,sv_pipeline_hail_docker
,sv_pipeline_updates_docker
,sv_pipeline_rdtest_docker
all now justsv_pipeline_docker
Downstream filtering
- Reduce SVConcordance memory usage
- Release AoU filtering model
- Make the ploidy table a workflow output instead of an intermediate
- Change Vapor bed preprocessing errors to warnings
- Genotype filtering training labels and cutoff optimization
Misc.
- Add ReshardVcf workflow
- Setup automatic updates to WDLs on Dockstore
- Trivial change to sv-pipeline-virtual-env
- Add a preview version of the de-novo pipeline
Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.4-beta...v0.28.5-beta
Files
broadinstitute/gatk-sv-v0.28.5-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/v0.28.5-beta (URL)