Welcome to v1.0 of GATK-SV! With this release, we are deprecating MELT in favor of Scramble, adding downstream filtering and refinement steps to the core pipeline and Terra workspace, moving our documentation to our website, and getting ready to release our public Terra workspace for the joint calling mode of GATK-SV.
Updates include
Pipeline functionality
- Improve Scramble accuracy for BWA and Dragen 3.7.8
- Refine complex variants and translocations
- Filter wham-only DELs and scramble-only SVAs in CleanVcf
- Update GATK to 4.6.0.0 in sv_pipeline_docker
- Resolve incorrect mCNV genotype counts for hom-alt
- Updates to EvidenceQC for sample QC analysis
- Enhance EvidenceQC outputs to better align with sample QC
- Add Scramble metrics to the qc table generated in EvidenceQC
- Rename high & low overall outliers columns generated via EvidenceQC
- Leave empty genotypes in CleanVcf part 5
- Add check for duplicate records to MainVcfQc
- Update type-checking in RdTestV2 to be class-based
Documentation
- Move documentation to website
- Update docs on creating sample_set_set
- Update GatherSampleEvidence & TrainGCNV docs
- Update the landing page of the docs
- Add genotype filtering Terra workflow configs and documentation
- Include SVTK documentation in README
For developers
- Deprecate Google Cloud configuration JSONs
- Add the single-sample pipeline to the Dockstore automation
Full Changelog: v0.29-beta...v1.0