Releases: broadinstitute/gatk-sv
Releases · broadinstitute/gatk-sv
v0.23-beta
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
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
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
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
Updates:
- Add TrainGCNV input specifying subset list of samples for training #294
v0.20.1-beta
Updates include: #290
v0.20-beta
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
v0.19.3-beta
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
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