v0.28-beta

Note: This version corresponding to v0.28-beta does not have updated docker images. The docker image updates are now reflected in v0.28.1-beta so that version should be used instead.

What's changed

Improvements to SR genotyping and INS breakpoints:

• Update SR counting and genotyping

Filtering workflows:

• Update ApplyManualVariantFilter json template
• Update VaPoR workflows
• SVConcordance workflows update
• Fix CTX END2 error in GATK formatting script

Other workflows:

• Fix non-deterministic errors in GetSampleIdsFromVcfTar
• make the RunMELT task a little more robust
• Improve STR workflow
• Remove DeleteIntermediateFiles task
• Remove unused ped_file input from GenotypeBatch and RegenotypeCNVs

Docker build:

• Manually install MASS R package in sv-pipeline-virtual-env
• Build and publish images to multiple registries in one job, & update the dependencies of the action

Other scripts, docs, and JSONs:

• Update copy_outputs.py
• Generate Terra workspace tsv files from transposed tables
• Update README to link to SV callers used
• Remove ped file from workspace data TSV for cohort mode terra workspace

Full Changelog: v0.27.3-beta...v0.28-beta

v0.27.3-beta

What's Changed

• Update README for docker build script
• Fix for tiny shard of IntegrateGQ in single sample pipeline
• Set minimum PE count of 1 during genotyping

Full Changelog: v0.27.2-beta...v0.27.3-beta

v0.27.2-beta

What's Changed

• Add missing space in functional annotation to enable optional settings
• Eliminate cram to bam conversion when possible
• Add ref panel inputs for MakeCohortVcf subworkflows
• Extend STR workflow to collect additional locus-level metrics
• Change ref allele to N if unsupported during vcf standardization
• Add sample renaming for SD files in GatherBatchEvidence
• Remove vcf header contig sorting in CleanVcf5
• Add support for building dockers for multiple registries
• Remove non-public images from the git-sha-based target determination in docker build script

Full Changelog: v0.27.1-beta...v0.27.2-beta

v0.27.1-beta

What's Changed

• Add handling for Flag vcf fields to vcf_to_pandas
• Add outlier samples list & count outputs to PlotSVCountsPerSample

Full Changelog: v0.27-beta...v0.27.1-beta

v0.27-beta

What's Changed

• New RdTest mode for very large variants
• Updates to the documentation website, its build action, and the Algolia configuration
• CleanVcfPart5 fix
• Add legacy file support for BatchEvidenceMerging

Full Changelog: v0.26.10-beta...v0.27-beta

v0.26.10-beta

Updates

• Update WDLs to adhere with implicit coercions requirement
• Update the style of build_docker.py
• Remove depth vcf from pesr merging in FilterBatchSamples
• Maintain a mirror of images on GCR and ACR
• Set target images for Azure based on commit SHA

Full Changelog: v0.26.9-beta...v0.26.10-beta

v0.26.9-beta

Updates

• Fixes an bug in the single sample pipeline that caused too many variants to be filtered with REF_PANEL_GENOTYPES
• Updates to GitHub Actions and the docker build process
• Includes mCNVs in per-sample QC plots in MainVcfQc

Full Changelog: v0.26.8-beta...v0.26.9-beta

v0.26.8-beta

Updates

• De-duplicate variant IDs in analyze_fams.R and improve style/spacing
• Add workflow to apply bcftools hard variant filter
• Add wrapper workflow to call SubsetVcfBySamplesList task to include or exclude a list of samples
• Update CollectSVEvidence argument names to match latest version of GATK tool

Full Changelog: v0.26.7-beta...v0.26.8-beta

v0.26.7-beta

• Fixes slight allele count bias in SD file generation
• Fixes SDToBAF filtering het sites too stringently

v0.26.6-beta

Updates

• Create CODE_OF_CONDUCT.md
• Combine multiple EvidenceQC outputs used for sample QC and batching into one convenient table

Full Changelog: v0.26.5-beta...v0.26.6-beta