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Releases: broadinstitute/gatk-sv

v0.24.1-beta

10 Aug 16:50
@epiercehoffman epiercehoffman
v0.24.1-beta
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v0.24.1-beta Pre-release
Pre-release

Updates

Two bug fixes in GenotypeComplexVariants: in ParseGenotyping and ConcatCpxCnvVcfs tasks

Full Changelog: v0.24-beta...v0.24.1-beta

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v0.24-beta

28 Jul 15:49
@epiercehoffman epiercehoffman
v0.24-beta
ef29ea1
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v0.24-beta Pre-release
Pre-release

Updates include:

  • ExpansionHunter: Improvements on scaling the EH WDL to more batches, Convert EH JSON to TSV
  • Docker build: Decrease disk usage building dockers on GitHub, Build STR docker image using the build_docker script, Decrease docker count, Enable docker build on m1 macs
  • svtk vcfcluster: Bug fixes, Performance optimization, Fix STRANDS and EV related errors
  • Add GqRecalibrator WDLs and input templates
  • Early BAF generation from CRAMs
  • Switch to new CondenseDepthEvidence GATK tool
  • Run the 5 subworkflows of MakeCohortVcf as separate steps in Terra
  • Integrate GATK SVCluster into ClusterBatch
  • Handle low PE cutoff in genotyping

Full Changelog: v0.23-beta...v0.24-beta

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v0.23-beta

04 May 19:30
@epiercehoffman epiercehoffman
v0.23-beta
daf14a9
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v0.23-beta Pre-release
Pre-release

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

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v0.22-beta

29 Apr 20:37
@epiercehoffman epiercehoffman
v0.22-beta
e6c21c5
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v0.22-beta Pre-release
Pre-release

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

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

14 Apr 18:48
@epiercehoffman epiercehoffman
v0.9.1-beta-hotfix2
87eee64
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Hotfix for v0.9.1-beta-hotfix: v0.9.1-beta-hotfix2 Pre-release
Pre-release

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.

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v0.21-beta

13 Apr 18:38
@epiercehoffman epiercehoffman
v0.21-beta
956ebac
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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

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v0.20.2-beta

11 Feb 16:49
@epiercehoffman epiercehoffman
v0.20.2-beta
a770cc7
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v0.20.2-beta Pre-release
Pre-release

Updates:

  • Add TrainGCNV input specifying subset list of samples for training #294
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v0.20.1-beta

03 Feb 19:40
@epiercehoffman epiercehoffman
v0.20.1-beta
ab8a855
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v0.20.1-beta Pre-release
Pre-release

Updates include: #290

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v0.20-beta

03 Feb 19:38
@epiercehoffman epiercehoffman
v0.20-beta
dd9f115
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v0.20-beta Pre-release
Pre-release

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

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v0.19.4-beta

14 Jan 18:04
@epiercehoffman epiercehoffman
v0.19.4-beta
aa6e2a0
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v0.19.4-beta Pre-release
Pre-release

Updates include:

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

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