v1.0.2

What's Changed

Core updates

• Update CombineBatches workflow
• Update to gnomAD-SV-v4 for external AF annotation
• Create SampleQC and Batching notebooks
• Remove internal workflows and scripts (migrated to gatk-sv-internal repo)

Bug fixes

• Fix handling of multiallelic GTs with low copy number
• Fix bug that results in an empty Vapor report
• Fix IntegrateGQ.sh errors due to presence of variants of just one type
• Reorder PED file columns in SampleQC notebook

Ease of use

• Add VCF input option to Vapor WDL
• Make functional annotation optional if no GTF/BED provided
• Small fixes to sample QC notebook

Documentation and input templates

• Updates to EvidenceQC templates
• Add joint calling link to documentation
• Remove mention of variant filtering from GenerateBatchMetrics documentation
• Update gatk docker on azure

Full Changelog: v1.0.1...v1.0.2