Releases: broadinstitute/gatk-sv
Releases · broadinstitute/gatk-sv
v0.26.5-beta
Updates include
- HailMerge womtool validation fix
- Replace EH version with its current latest release
- Update WDLs to adhere with the miniwdl requirements and add miniwdl validation to CI/CD
- Add VisualizeCnvs workflow
- GATK vcf formatting script fixes
- Install git lfs and add tracking png and jpg files
Full Changelog: v0.26.4-beta...v0.26.5-beta
v0.26.4-beta
Updates
- Various updates to make WDLs validate with MiniWDL
- Fix issues in definitions of pesr exclude list and sd files in single sample pipeline Terra workspace template files
- Update terra pipeline diagram to reflect v0.26.3-beta
- ExpansionHunter: Fix a bug in generating realigned BAM in the output of EH, add support for the seeking option, create an empty timing file in case it is not created, change the default max depth of inheritance & update help
- Update gatk to include CollectSVEvidence bug fix
- Hook up WGD runtime attribute overrides
Full Changelog: v0.26.3-beta...v0.26.4-beta
v0.26.3-beta
Updates
- Various small fixes to documentation
- Add genotype concordance workflows
Full Changelog: v0.26.2-beta...v0.26.3-beta
v0.26.2-beta
Updates
- Option to map between internal and external sample IDs for per-sample benchmarking in MainVcfQc
- Set disk to at least 10 gb in VaPoR tasks
Full Changelog: v0.26.1-beta...v0.26.2-beta
v0.26.1-beta
Updates
- Option to input & subset multi-sample BED in VaPoR (+ womtool fixes)
Full Changelog: v0.26-beta...v0.26.1-beta
v0.26-beta
What's Changed
- Adds sv-utils, a python package that supports GQ filtering and benchmarking, and updates the GQ filtering WDLs
- Removes Delly and related commands from the pipeline
- Fixes a bug in the single sample pipeline caused by records with missing depth genotypes and no PE or SR support
- Improves ExpansionHunter JSON to TSV conversion when the JSON is missing LocusResults
- Improvements to the script validating WDLs using miniwdl
Full Changelog: v0.25.1-beta...v0.26-beta
v0.25.1-beta
Updates
- Log a warning when merging EH JSON files if a file does not contain LocusResult
- Standardize scramble output
Full Changelog: v0.25-beta...v0.25.1-beta
v0.25-beta
Updates
- Rework MasterVcfQc --> now MainVcfQc with enhanced functionality
- Modify VaPoR settings
- MiniWDL validation script
Full Changelog: v0.24.3-beta...v0.25-beta