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Releases: broadinstitute/gatk-sv

v0.26.5-beta

30 Nov 20:30
65a0ea3
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v0.26.5-beta Pre-release
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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

12 Oct 15:45
89a5fc5
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v0.26.4-beta Pre-release
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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

27 Sep 23:09
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v0.26.3-beta Pre-release
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Updates

  • Various small fixes to documentation
  • Add genotype concordance workflows

Full Changelog: v0.26.2-beta...v0.26.3-beta

v0.26.2-beta

22 Sep 16:59
8bd8d4a
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v0.26.2-beta Pre-release
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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

19 Sep 17:07
90e3e9a
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v0.26.1-beta Pre-release
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Updates

  • Option to input & subset multi-sample BED in VaPoR (+ womtool fixes)

Full Changelog: v0.26-beta...v0.26.1-beta

v0.26-beta

16 Sep 14:40
2da5e29
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v0.26-beta Pre-release
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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

08 Sep 16:11
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v0.25.1-beta Pre-release
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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

26 Aug 19:07
3f269e8
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v0.25-beta Pre-release
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Updates

  • Rework MasterVcfQc --> now MainVcfQc with enhanced functionality
  • Modify VaPoR settings
  • MiniWDL validation script

Full Changelog: v0.24.3-beta...v0.25-beta

v0.24.3-beta

22 Aug 19:41
1f03eea
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v0.24.3-beta Pre-release
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Updates

  • Improve on Scramble integration

Full Changelog: v0.24.2-beta...v0.24.3-beta

v0.24.2-beta

18 Aug 18:48
ccceea0
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v0.24.2-beta Pre-release
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Updates

  • Output VaPoR header with # in front

Full Changelog: v0.24.1-beta...v0.24.2-beta