v0.26.3-beta

Updates

• Various small fixes to documentation
• Add genotype concordance workflows

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

v0.26.2-beta

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

Updates

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

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

v0.26-beta

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

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

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

Updates

• Improve on Scramble integration

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

v0.24.2-beta

Updates

• Output VaPoR header with # in front

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

v0.24.1-beta

Updates

Two bug fixes in GenotypeComplexVariants: in ParseGenotyping and ConcatCpxCnvVcfs tasks

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

v0.24-beta

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