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Releases: broadinstitute/gatk-sv

v0.23-beta

04 May 19:30
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v0.23-beta Pre-release
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Updates

  • Increment the EH version in its Dockerfile to the current latest release
  • Increase memory in PostprocessGermlineCNVCalls to original
  • Check for scramble in breakpoint overlap filter
  • Use GATK tool SVAnnotate for functional consequence annotation

Full Changelog: v0.22-beta...v0.23-beta

v0.22-beta

29 Apr 20:37
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v0.22-beta Pre-release
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Updates:

  • Fix ENDs and rescale GQ to [0,99] at end of CleanVcf
  • Authentication for CI/CD bot to update docker images
  • Replace Array[File] with File inputs in single-sample pipeline

Full Changelog: v0.21-beta...v0.22-beta

Hotfix for v0.9.1-beta-hotfix: v0.9.1-beta-hotfix2

14 Apr 18:48
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Hotfix for previous release v0.9.1-beta-hotfix: the state of the pipeline is the same as release v0.9.1-beta-hotfix but fixes a regression in Whamg.wdl. See #332. This tag does not reflect the latest version of the GATK-SV pipeline.

v0.21-beta

13 Apr 18:38
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v0.21-beta Pre-release
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Updates include

  • Single sample pipeline fixes for MakeCohortVcf
  • Add minGQ_NCR INFO field
  • Migrate to 1KGP reference panel for testing
  • Build docker updates
  • Add option to run Scramble
  • GATK docker updates
  • Option to provide credentials JSON to access CRAMs
  • Fix bug in Whamg

Full Changelog: v0.20.2-beta...v0.21-beta

v0.20.2-beta

11 Feb 16:49
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v0.20.2-beta Pre-release
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Updates:

  • Add TrainGCNV input specifying subset list of samples for training #294

v0.20.1-beta

03 Feb 19:40
ab8a855
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v0.20.1-beta Pre-release
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Updates include: #290

v0.20-beta

03 Feb 19:38
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v0.20-beta Pre-release
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Updates include: Scaling updates and bug fixes to MakeCohortVcf implemented as part of processing gnomAD-SV-v3.

Full Changelog: v0.19.4-beta...v0.20-beta

v0.19.4-beta

14 Jan 18:04
aa6e2a0
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v0.19.4-beta Pre-release
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Updates include:

Full Changelog: v0.19.3-beta...v0.19.4-beta

v0.19.3-beta

21 Dec 20:17
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v0.19.3-beta Pre-release
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Changes include:

  • remove bgzip for already-gzipped file in XfBatchEffect.GetFreqTable in #270
  • Add subset ped step at start of CleanVcf in #250

Full Changelog: v0.19.2-beta...v0.19.3-beta

v0.19.2-beta

29 Nov 22:28
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v0.19.2-beta Pre-release
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Updates include:

  • Drop variants with NA scores in FilterBatchSites
  • Efficiency fix for getting male-only variants on chrX in GenerateBatchMetrics
  • Docker build updates

Full Changelog: v0.19.1-beta...v0.19.2-beta