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Commits on Nov 4, 2022

• GATK vcf formatting script fixes (broadinstitute#452)

  mwalker174

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• Add VisualizeCnvs (broadinstitute#423)

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Commits on Oct 11, 2022

• Hook up WGD run attribute overrides (broadinstitute#442)

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Commits on Sep 27, 2022

• Genotype concordance workflows (broadinstitute#414)

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  1f1a3b3

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Commits on Aug 8, 2022

• Bug fix for ParseGenotyping (broadinstitute#381)

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Commits on Jul 25, 2022

• Integrate GATK SVCluster into ClusterBatch (broadinstitute#346)

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Commits on Jun 27, 2022

• Allow no-call alleles in genotype selection; fix String INFO field merging (broadinstitute#362)

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Commits on Jun 22, 2022

• Increase expected number of validated Terra jsons to 21 (broadinstitute#361)

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Commits on Jun 17, 2022

• Fix STRANDS and EV related errors in svtk vcfcluster (broadinstitute#359)

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Commits on May 4, 2022

• Check for scramble in breakpoint overlap filter (broadinstitute#344)

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Commits on Mar 28, 2022

• Add scramble docker input (broadinstitute#322)

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Commits on Mar 22, 2022

• Delete microsoft R mirror (broadinstitute#317)

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• Add MakeCohortVcf.vcf_qc output to batch workflow (broadinstitute#318)

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Commits on Mar 7, 2022

• Fix default dockers.json path in docker scripts (broadinstitute#302)

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Commits on Mar 4, 2022

• Revert gatk dockers to 4.1.8.1 (broadinstitute#301)

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• Migrate to 1KGP reference panel for testing (broadinstitute#293)

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Commits on Mar 2, 2022

• Optimize trio ID filtering in optimize_minGQ_ROC_v2.R (broadinstitute#300)

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• Add minGQ_NCR INFO field (broadinstitute#297)

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Commits on Feb 23, 2022

• Single sample pipeline fixes for MakeCohortVcf (broadinstitute#295)

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• Fix SubsetLarge output prefix in MergePesrDepth.wdl (broadinstitute#296)

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Commits on Feb 2, 2022

• Second round of MakeCohortVcf updates from gnomAD (broadinstitute#288)

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Commits on Nov 29, 2021

• Filter sites with NA score (broadinstitute#267)

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Commits on Sep 10, 2021

• MakeCohortVcf updates from gnomAD-SV (broadinstitute#216)

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Commits on Jul 26, 2021

• Allow missing vcf samples or gvcfs in Module00c (broadinstitute#207)

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• Fix svtest vcf pass evaluation (broadinstitute#197)

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Commits on Jul 6, 2021

• Add regenotyped depth vcf indexes to Module04b output (broadinstitute#192)

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Commits on Jun 15, 2021

• Support original sample ids in snp vcfs (broadinstitute#186)

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Commits on Jun 14, 2021

• Delete unused requirements.txt for igv docker (broadinstitute#171)

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• module00b updated to generate median bincov (broadinstitute#174)

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  xuefzhao

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Commits on May 19, 2021

• Fix SR_GQ assignment in cleanvcf4 (broadinstitute#170)

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Commits on May 11, 2021

• Remove GCS authentication from ZPaste in MakeBincovMatrix (broadinstitute#152)

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Commits on Apr 16, 2021

• Update to Modules 07-09 and add Module10 (broadinstitute#150)

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Commits on Mar 2, 2021

• Fix Module0506 inputs for Batch and SingleSample wdls (broadinstitute#118)

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  henriqueribeiro

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Commits on Feb 3, 2021

• Split 0506 into stages, remove 05_06 underscore in wdls (broadinstitute#88)

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Commits on Dec 23, 2020

• Add SV count outlier cutoff table to Module03 and bug fix for MasterVcfQC (broadinstitute#90)

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  xuefzhao

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