Releases | Open Source Science

https://github.com/broadinstitute/gatk-sv - v1.1

GATK-SV v1.1 includes major single-sample pipeline upgrades such as improved filtering and a new reference panel, alongside updates to the joint calling pipeline.

Updates include

Single-sample pipeline

Single-sample pipeline updates
- Add filtering
- New reference panel
- Run Scramble by default
- Reference panel creation notebook
- and more
Revert format detection changes to MakeBincovMatrix

Joint-calling pipeline functionality

Enable DRAGEN-SV as a caller in cohort mode
Enable outlier sample exclusion from training in TrainGCNV and GenerateBatchMetrics
Add denoised copy number plots and stratified variant counts to EvidenceQc outputs

Minor changes and bug fixes

Zip regeno coverage medians file
Update SVConcordance.wdl to enable stratified matching
Update reference genome in depth plots
Fix code path in EvidenceQc when run_ploidy is false
Bug fix missing sample ID in median coverage
Enable passing a threshold to govern the window for detection of dispersed deletions
Handle zero-length arrays in JoinRawCalls

sv-shell (WDL-independent pipeline-in-progress)

WDL-independent version of GatherSampleEvidence
Log stdout and stderr of tasks in sv_shell
Implement a bash version of the Evidence QC workflow

CI/CD

Disable automated sv-shell and scramble docker updates temporarily while addressing R package installation issues

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.5...v1.1

- Python
Published by epiercehoffman 6 months ago

https://github.com/broadinstitute/gatk-sv - v1.0.5

What's Changed

Bug fixes

Remove sorting from SVConcordance to align with the updated GATK tool
Keep EV as int when reformatting legacy genotyped VCFs

Miscellaneous

Update image links to address page scrolling issues on our website
Fix typo in argument in stitchfragmentedCNVs.sh
Update issue templates
Update shell flags for consistency and deprecate outdated bincov code path in MakeBincovMatrix
Fix BND header description
Deprecate ShardedCluster.wdl

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.4...v1.0.5

- Python
Published by epiercehoffman 8 months ago

https://github.com/broadinstitute/gatk-sv - v1.0.4

What's Changed

Critical

The AnnotateVcf workflow configuration in Terra has been corrected to take the filtered VCF as input. * If you have processed a cohort with GATK-SV in Terra and you have run FilterGenotypes, you should be aware that the AnnotateVcf output may not be filtered. * You can tell whether a VCF has been through filtering by looking for the NCR INFO field in the header - if it’s there, FilterGenotypes has been applied. * To address this, copy the updated AnnotateVcf workflow from the featured workspace to get the new input configuration, and update the gatk_docker in Workspace Data to match the featured workspace.

Bug fixes

Update GATK docker with CPX interval sorting fix for SVAnnotate
CPU configuration workaround for RealignSoftClippedReads
Enable non-existent INFO/EVIDENCE fields in input VCF for breakpoint overlap filtering in ResolveComplexVariants

Miscellaneous

Remove hail-based VCF merging
Update website regarding GATK forum

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.3...v1.0.4

- Python
Published by epiercehoffman 9 months ago

https://github.com/broadinstitute/gatk-sv - v1.0.3

What's changed

Critical

This release includes a fix for a bug introduced in v1.0.2 that affects GQ values and may have impacts on filtering. We recommend that users who ran the CombineBatches workflow with version v1.0.2 or v1.0.2-hotfix should update CombineBatches and CleanVcf to v1.0.3 and rerun the workflows from CombineBatches until the end of the pipeline. More details in #796.

Pipeline resources

Update GTF to GENCODE v47, and add reusable GTF preprocessing script

Bug fixes

Address rare edge cases in RefineComplexVariants
Fix MainVcfQc.IdentifyDuplicates to resolve NoneType mismatches

CI/CD

Update the OS version of the Action runners, and make the corresponding changes to the docker build CI/CD action
Add the de novo pipeline to Dockstore integration
Remove carrot tests
Use communicate() with Python subprocess

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.2-hotfix...v1.0.3

- Python
Published by epiercehoffman 11 months ago

https://github.com/broadinstitute/gatk-sv - v1.0.2-hotfix

This release is a hotfix addressing a bug introduced in v1.0.2 that caused ClusterBatch to fail.

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.2...v1.0.2-hotfix

- Python
Published by epiercehoffman about 1 year ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v1.0.1...v1.0.2

- Python
Published by epiercehoffman about 1 year ago

https://github.com/broadinstitute/gatk-sv - v1.0.1

What's Changed

Bug fixes

Fix for normalize_counts() in GenerateBatchMetrics
Modify EvidenceQC to not create/expect additional column in median coverage file
Fix multiallelic genotypes for biallelic CNVs

Documentation

Add links to GATK forums and joint calling workspace
Replace relative paths with abs paths to JS components

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0...v1.0.1

- Python
Published by epiercehoffman over 1 year ago

https://github.com/broadinstitute/gatk-sv - v1.0

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 svpipelinedocker
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 samplesetset
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: https://github.com/broadinstitute/gatk-sv/compare/v0.29-beta...v1.0

- Python
Published by epiercehoffman over 1 year ago

https://github.com/broadinstitute/gatk-sv - v0.29-beta

What's Changed

Critical

This release includes a critical bug fix to the SplitVariants task in GenotypeBatch. The affected workflow was GenotypeBatch, and the affected version was v0.28.5-beta. We recommend immediately updating to v0.29-beta. If you ran GenotypeBatch with v0.28.5-beta, please check if any records were dropped. If in doubt, re-run with v0.29-beta. More details in #712

Pipeline functionality updates

Integrate ReshardVcf into ResolveComplexVariants
Remove CHR2 and END2 from INS in CleanVcf
Fix --par arg to compute_AFs.py in ShardedAnnotateVcf
Updates to allele frequency annotation fields
Grouped MEIs with insertions in splitvariants.py

Performance improvements

Reimplement ParseGenotypes in GenotypeComplexVariants
Reduce memory usage in GenotypeSRPart1
Set the default disk size in AnnotateIntervals as a function of input files size
Making the Vapor plots optional to store as a final output
Make per-sample QC plots optional in MainVcfQc

Fixing bugs and small annoyances

Skip subsampling if batch size is less than nsamplessubsample
Add NonZeroReferenceLengthAlignmentReadFilter read filter to CollectSVEvidence
Prevent sample ID mangling in WGD computation
Update gatk docker with changes to handle CPX_TYPE for CTX
Fix UnboundLocalError in EvidenceQc
Update gnomad-v2 sample-level benchmarking data path

Documentation

Terra dashboard updates
Reorganize docs on running the pipeline
Add CONTRIBUTING.md
Update Docusaurus and its dependencies to v3.3.2
Update docs on building and hosting Docker images
Update docs on building inputs
Add documentation for rename_samples in GatherBatchEvidence

CI/CD, workflow organization, and auxiliary scripts

Deprecate single-batch Terra configs
Add support for incomplete workflows in getinputsoutputs.py
Trigger WDL tests on changes to /inputs and fix Terra config tests
Update deprecated Pandas append operation for monitoring log analysis
Extend the list supported syntax-highlighting languages

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.5-beta...v0.29-beta

- Python
Published by epiercehoffman over 1 year ago

https://github.com/broadinstitute/gatk-sv - v0.28.5-beta

Updates

GatherSampleEvidence * Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES * Make LocalizeReads optional * Make manta region bed index required * Make MELT scripts independent of the execution path

Main pipeline * Rewrite SplitVariants in TasksGenotypeBatch.wdl * Disable MakeCohortVcfMetrics by default * Find CN field for mCNVs in MainVcfQc without hard-coding order of format fields * Update BEDTools version to 2.31.0 * Two small bugfixes to EvidenceQc * Update gatkdocker with CPX annotation changes to SVAnnotate * Reduce redundant docker image inputs: `svpipelinebasedocker,svpipelinehaildocker,svpipelineupdatesdocker,svpipelinerdtestdockerall now justsvpipeline_docker`

Downstream filtering * Reduce SVConcordance memory usage * Release AoU filtering model * Make the ploidy table a workflow output instead of an intermediate * Change Vapor bed preprocessing errors to warnings * Genotype filtering training labels and cutoff optimization

Misc. * Add ReshardVcf workflow * Setup automatic updates to WDLs on Dockstore * Trivial change to sv-pipeline-virtual-env * Add a preview version of the de-novo pipeline

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.4-beta...v0.28.5-beta

- Python
Published by epiercehoffman almost 2 years ago

https://github.com/broadinstitute/gatk-sv - v0.28.4-beta

Updates include

SV discovery algorithms: * Update manta to 1.6.0 * Optimize Scramble

New functionality: * Add PED file validation to GatherBatchEvidence and as standalone script

Documentation and CI/CD: * Add Scramble docker to the build script & update docs * Clarify single-batch vs. multi-batch workflows in cohort mode Terra workspace on dashboard

Updates and bug fixes: * Remove redundant GetPed task in GatherBatchEvidence.CNMOPS * Make genometracks optional in FilterGenotypes * Toggle Collect PESR/Counts in GatherSampleEvidence with booleans * Fix allosomeslist bug * Filter mCNVs under 5kbp * Remove hgdp1kgpped test batch input from MainVcfQc template * Fix melt insert size input type in EvidenceQC * Correct use of optimizevcfrecordspershard in FilterGenotypes * Update JoinRawCalls formatter arg in template * Check for empty scatter in GenotypeDepthPart2 * Make the Cromwell root config in the MELT workflow portable

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.3-beta...v0.28.4-beta

- Python
Published by epiercehoffman over 2 years ago

https://github.com/broadinstitute/gatk-sv - v0.28.3-beta

Updates include

Remove CHR2 and END2 for CPX at the end of CleanVcf
Add TSV rename map option to RenameVcfSamples
Add required index files to hg38 resources
Add Docker images build instructions to the docs
Add PlotSVCountsPerSample subworkflow to the end of ClusterBatch and FilterBatchSites

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.2-beta...v0.28.3-beta

- Python
Published by epiercehoffman over 2 years ago

https://github.com/broadinstitute/gatk-sv - v0.28.2-beta

Updates include

Add high-level description of docker images and their build process
Remove max GQ filtering from per sample QC
Update protein-coding GTF to MANE v1.2
Reference panel resources and critical bug fixes
Add FilterGenotypes workflow
Remove use of the file command
Move PESR genotyping filter statuses to info fields
Bug fix building samtools-cloud docker
Bug fix Github actions out of disk error
Sharded AnnotateVcf workflow
Add Terra validation to Github actions
Resolve new linting errors
Deduplicate records and CPX variant IDs in ResolveComplexVariants

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.1-beta...v0.28.2-beta

- Python
Published by epiercehoffman over 2 years ago

https://github.com/broadinstitute/gatk-sv - v0.28.1-beta

This release incorporates the updated docker images from v0.28-beta.

Updates

Fix a bug committing changes to dockers_*.json after an image is updated
Delete some commented lines in dropemptyrecords.py to prompt docker build

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28-beta...v0.28.1-beta

- Python
Published by epiercehoffman over 2 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.27.3-beta...v0.28-beta

- Python
Published by epiercehoffman over 2 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.27.2-beta...v0.27.3-beta

- Python
Published by epiercehoffman almost 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.27.1-beta...v0.27.2-beta

- Python
Published by epiercehoffman almost 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.27.1-beta

What's Changed

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

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.27-beta...v0.27.1-beta

- Python
Published by epiercehoffman almost 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.26.10-beta...v0.27-beta

- Python
Published by epiercehoffman almost 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.26.9-beta...v0.26.10-beta

- Python
Published by epiercehoffman almost 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.9-beta

Updates

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

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26.8-beta...v0.26.9-beta

- Python
Published by cwhelan about 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.26.7-beta...v0.26.8-beta

- Python
Published by epiercehoffman about 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.7-beta

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

- Python
Published by mwalker174 about 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.6-beta

Updates

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

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26.5-beta...v0.26.6-beta

- Python
Published by epiercehoffman about 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.5-beta

Updates include

HailMerge womtool validation fix
Replace EH version with its current latest release
Update WDLs to adhere with the miniwdl requirements and add miniwdl validation to CI/CD
Add VisualizeCnvs workflow
GATK vcf formatting script fixes
Install git lfs and add tracking png and jpg files

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26.4-beta...v0.26.5-beta

- Python
Published by epiercehoffman about 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.4-beta

Updates

Various updates to make WDLs validate with MiniWDL
Fix issues in definitions of pesr exclude list and sd files in single sample pipeline Terra workspace template files
Update terra pipeline diagram to reflect v0.26.3-beta
ExpansionHunter: Fix a bug in generating realigned BAM in the output of EH, add support for the seeking option, create an empty timing file in case it is not created, change the default max depth of inheritance & update help
Update gatk to include CollectSVEvidence bug fix
Hook up WGD runtime attribute overrides

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26.3-beta...v0.26.4-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.3-beta

Updates

Various small fixes to documentation
Add genotype concordance workflows

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26.2-beta...v0.26.3-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.26.1-beta...v0.26.2-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.26.1-beta

Updates

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

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.26-beta...v0.26.1-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.25.1-beta...v0.26-beta

- Python
Published by cwhelan over 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.25-beta...v0.25.1-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.25-beta

Updates

Rework MasterVcfQc --> now MainVcfQc with enhanced functionality
Modify VaPoR settings
MiniWDL validation script

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.24.3-beta...v0.25-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.24.3-beta

Updates

Improve on Scramble integration

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.24.2-beta...v0.24.3-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.24.2-beta

Updates

Output VaPoR header with # in front

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.24.1-beta...v0.24.2-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - v0.24.1-beta

Updates

Two bug fixes in GenotypeComplexVariants: in ParseGenotyping and ConcatCpxCnvVcfs tasks

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.24-beta...v0.24.1-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.23-beta...v0.24-beta

- Python
Published by epiercehoffman over 3 years ago

https://github.com/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: https://github.com/broadinstitute/gatk-sv/compare/v0.22-beta...v0.23-beta

- Python
Published by epiercehoffman almost 4 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.21-beta...v0.22-beta

- Python
Published by epiercehoffman almost 4 years ago

https://github.com/broadinstitute/gatk-sv - 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.

- Python
Published by epiercehoffman almost 4 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.20.2-beta...v0.21-beta

- Python
Published by epiercehoffman almost 4 years ago

https://github.com/broadinstitute/gatk-sv - v0.20.2-beta

Updates: * Add TrainGCNV input specifying subset list of samples for training #294

- Python
Published by epiercehoffman about 4 years ago

https://github.com/broadinstitute/gatk-sv - v0.20.1-beta

Updates include: #290

- Python
Published by epiercehoffman about 4 years ago

https://github.com/broadinstitute/gatk-sv - v0.20-beta

Updates include: Scaling updates and bug fixes to MakeCohortVcf implemented as part of processing gnomAD-SV-v3.

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.19.4-beta...v0.20-beta

- Python
Published by epiercehoffman about 4 years ago

https://github.com/broadinstitute/gatk-sv - v0.19.4-beta

Updates include: * Tweaks to AnnotateVcf workflow (#283) * Updates to ExpansionHunter (#276, #281, #282) * CI/CD updates (#268, #273)

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.19.3-beta...v0.19.4-beta

- Python
Published by epiercehoffman about 4 years ago

https://github.com/broadinstitute/gatk-sv - v0.19.3-beta

Changes include: * remove bgzip for already-gzipped file in XfBatchEffect.GetFreqTable in https://github.com/broadinstitute/gatk-sv/pull/270 * Add subset ped step at start of CleanVcf in https://github.com/broadinstitute/gatk-sv/pull/250

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.19.2-beta...v0.19.3-beta

- Python
Published by epiercehoffman about 4 years ago

https://github.com/broadinstitute/gatk-sv - 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: https://github.com/broadinstitute/gatk-sv/compare/v0.19.1-beta...v0.19.2-beta

- Python
Published by epiercehoffman about 4 years ago