Genotyping Workflow and AnnotSV Updates

GATK Genotyping Workflow Update

This release updates the GATK Genotyping portion of our germline variant workflow. Previously the workflow had been written only with WGS samples in mind. This release updates the workflow so it can handle WXS and Targeted Sequencing inputs. The key difference between WGS and WXS/Targeted calling is in the variant filtration process. WGS samples will be processed using VQSR; WXS/Targeted samples will be processed using HardFiltering. Users can now specify the experiment_type of the input and the workflow will perform the appropriate filtration.

Accompanying this update, we've also added a new output called gatk_annotation_plots. This TAR.GZ file contains a series of plots of the key genotying annotations used for the HardFiltering process. As it is associated with HardFiltering, this output will only be created if the sample is WXS/Targeted.

We've also updated the GATK dockers used for a number of the utility functions used in the genotyping workflow. These functions include gathering VCFs, tranches, etc and should have no impact on the final outputs.

Other Functional Updates

• Two new outputs to the germline workflow:
  • AnnotSV-annotated version of CNVnator's cnvnator_vcf output
  • AnnotSV-annotated version of GATK's gatk_gcnv_genotyped_segments_vcfs output
• Adjustments were made to the germline workflow to make some inputs no longer required; since pretty much everything can be turned off/on, requirements mostly depend on what you are trying to do
• Opened extra argument ports for various tools in the workflow. Gives the user more control of the run

Documentation Updates

This release also contains a series of documentation updates:

• Fixing the Broad GCP links in the docs
• Updated docs to include new outputs

What's Changed

• 📚 update gcp docs by @dmiller15 in #48
• 🎉 add annotsv to CNVnator and docs by @dmiller15 in #49
• 🔧 annotsv gatk gcnv out by @dmiller15 in #50
• 🔧 GenomicsDBImport extra args init by @dmiller15 in #52
• 🤖 add docker table builder ghas by @dmiller15 in #54
• 🚧 exome/panel genotyping by @dmiller15 in #53
• 🎉 add hardfilter annotation filter plotting by @dmiller15 in #59
• 🐳 update gatk dockers by @dmiller15 in #61
• 🔖 genotyping release prep by @dmiller15 in #64

Full Changelog: v1.1.1...v1.2.0

🧹 Input and submodule cleanup

Removed a ClinVar suggested file as it's no longer KF SOP to run in prod.
Point to latest annotation submodule to incorporate latest changes

What's Changed

• ✨ plink init by @dmiller15 in #44
• 🔧 adjust plink workflow by @dmiller15 in #45
• 🧹 rm no longer needed clinvar defaults by @migbro in #46
• ✏️ update git release and kf-annot-submodule by @migbro in #47

Full Changelog: v1.1.0...v1.1.1

Annotation Refactor

• Minor bug fix for interval output and doc links
• added more annotSV outputs and added header to CNVnator output
• Refactor annotation to new standard
  • Dropped CADD, ClinVar, Intervar
  • Replaced gnomAD with custom built echtvar reference. See https://github.com/kids-first/kf-annotation-tools/blob/master/docs/CUSTOM_GNOMAD_REF.md
  • Made annotation repo a submodule

What's Changed

• 🐛 fix interval output by @dmiller15 in #38
• ✨ Add somalier relate by @migbro in #39
• ✨ add cnvnator call colnames by @dmiller15 in #40
• 🎉 annotsv on sv indel calls by @dmiller15 in #41
• 📚 fix doc links by @dmiller15 in #42
• 💫 Refactor Annotation by @migbro in #43

Full Changelog: v1.0.0...v1.1.0

KFDRC Germline Variant Worklfows

New All-in-one Workflow!

This release introduces the first all-in-one germline variant workflow for Kids First. The workflow wraps callers for CNV, SNV, and SV into a comprehensive production workflow. Please see the primary workflow documentation for information about the callers and methods.

Additional Fixes

We have updated the ClinVar reference. The old reference was missing several records and should not be used. Please delete it if you still have it.

Also:

• Most tools and workflows received upgrades to cwl 1.2
• Outputs were simplified and renamed for clarity

What's Changed

• 🐛 tumor-only/germline enabled by @dmiller15 in #29
• 🔧 fixes from benchmarking by @dmiller15 in #30
• 💽 modernize cnv wfs by @dmiller15 in #31
• ✨ germline variant workflow by @dmiller15 in #32
• ✨ annotate snvs by @dmiller15 in #33
• ✨ gvcf optional by @dmiller15 in #34
• 📚 release prep by @dmiller15 in #35
• 🏷️ update out names by @dmiller15 in #36
• 🐛 Fix ClinVar Input by @migbro in #37

Full Changelog: v0.4.4...v1.0.0

📖 Updated Default Cavatica Refs

We recently exported our files to a bucket. This update points the default file pulled to the new location. Functionality is unchanged, but a couple files may not auto-populate if a user uses an older version.

What's Changed

• 📖 Changed Default Ref Location After Export by @migbro in #28

Full Changelog: v0.4.3...v0.4.4

✏️ Set new default for tool name

Mostly for ops purposes, added clarity by updating the default tool name. The previous tool name default implied certain tools not used in this workflow.

What's Changed

• 🔧 Update file ext default to new spec by @migbro in #27

Full Changelog: v0.4.2...v0.4.3

🤏 Minor file naming update

Satisfies an Ops request to allow the tool_name input to determine the suffix and drop the default suffix added by the annotation workflow

What's Changed

• ✏️ allow tool_name to do the heavy lifting by @migbro in #26

Full Changelog: v0.4.1...v0.4.2

🐛 Fixed default file reference

A small update that addresses the following:

• Corrected the default secondaryFile for the CADD SNV input
• Added a default value for tool name for ease of use

What's Changed

• 🔧 Bug/fix secondary file ref by @migbro in #25

Full Changelog: v0.4.0...v0.4.1

Annotation Upgrade

In an effort to standardize annotation for both DNA and RNA, this adds a new annotation workflow.

• Added standalone wf with ability to strip old annotations to avoid conflicts and re-use old calls
• Upgraded from VEP 93 to VEP 105
• Incorporated workflow into single sample calling
• Added updated gnomad, clinvar, and dbsnsfp and intervar references to enhance "off-the-shelf" usability for downstream germline users

What's Changed

• 🚀 Add germline SNV Workflow by @migbro in #23
• 💪 Add annotation workflow and upgrade by @migbro in #24

Full Changelog: v0.3.0...v0.4.0

KFDRC Germline Structural Variant Workflow

KFDRC Germline Structural Variant Workflow

The primary focus of this release if the creation of a preliminary Germline Structural Sariant (SV) workflow. The workflow is runs two callers: Manta and SVaba. Both callers report two VCFs: one containing the smaller indels and another reporting the larger structural variations. Records from the latter files that can be annotated are done so by AnnotSV and reported in separate TSVs.

What's Changed

• 🎉 added vcf2parquet tool by @migbro in #19
• Feature/mb add sommalier by @migbro in #20
• 🔧 germline sv update by @dmiller15 in #21
• 📚 germline sv release prep by @dmiller15 in #22

New Contributors

• @migbro made their first contribution in #19

Full Changelog: v0.2.0...v0.3.0