feat: small updates oncogenic, dux4 and QC thresholds

[mathiasbio]

Description

This PR adds a few of small fixes / updates.

• There's a request from Scout to add a GT field to IGH-DUX4 variants which is required for some cross-case filtering: Matching causative IGH::DUX4 not displayed on case page - works from variant page #1515
• Then there's the new ONC fields from Clinvar which can be useful for clinicians when interpreting variants in Scout: [User Story] Add new oncogenic values from clinvar #1502
• Merged this PR into this one for easier testing: chore: update qc thresholds #1477
• This is the issue for the above PR: [User Story] Quick adjustments of QC thresholds #1373

Added

• New ONC annotations from Clinvar

Changed

• Added GT field to IGH-DUX4 variant
• Changed QC thresholds for WGS normal and WES

Documentation

• N/A
• Updated Balsamic documentation to reflect the changes as needed for this PR.
  • [balsamic_annotations.rst]

Tests

Feature Tests

ONC annotations:

• Verify that all fields from ONC can be annotated in the VCF
• ONC found ONC=Uncertain_significance
• ONCDN found ONCDN=Neoplasm
• ONCREVSTAT found ONCREVSTAT=criteria_provided,_single_submitter
• ONCDISDB found. ONCDISDB=Human_Phenotype_Ontolog....
• ONCCONF (does not exist in any variant of the most recent clinvar we downloaded and cannot be tested)

IGH-DUX4 changes

• Verify that the IGH-DUX4 variant can still be uploaded to Scout from old validation case

Uploaded to scout-stage on cust000

QC thresholds

• Verify that new QC thresholds are working
• WGS normal median coverage
• WGS 5 AT_DROPOUT
• WGS 5 GC_DROPOUT
• WES 10 AT_DROPUT
• WES 10 GC_DROPOUT

See more info in google sheet: https://docs.google.com/spreadsheets/d/1zMTxhPLFD8nVxWSjgtnb8iOmcJm31sX2I8n89nGJ02s/edit?gid=0#gid=0

Pipeline Integrity Tests

• Report deliver (generation of the .hk file)
  • N/A
  • Verified
• TGA T/O Workflow
  • N/A
  • Verified
• TGA T/N Workflow
  • N/A
  • Verified
• UMI T/O Workflow
  • N/A
  • Verified
• UMI T/N Workflow
  • N/A
  • Verified
• WGS T/O Workflow
  • N/A
  • Verified
• WGS T/N Workflow
  • N/A
  • Verified
• QC Workflow
  • N/A
  • Verified
• PON Workflow
  • N/A
  • Verified

Clinical Genomics Stockholm

Documentation

• Atlas documentation
  • N/A
  • Updated QC section: https://github.com/Clinical-Genomics/atlas/pull/3302
• Web portal for Clinical Genomics
  • N/A
  • Updated: [Link]

Panel of Normal specific criteria

• The PR includes the addition of a new Panel of Normals
• The samples have been verified to adhere to the sample selection criteria on Atlas PoN creation instructions for Balsamic

User Changes

• N/A
• This PR affects the output files or results.
  • User feedback is considered unnecessary because: we're only adding annotation information
  • Affected users have been included in the development process and given a chance to provide feedback.

Infrastructure Changes

• Stored files in Housekeeper
  • N/A
  • Updated: [Link]
• CG (CLI and delivered/uploaded files)
  • N/A
  • Updated: [Link]
• Servers (configuration files on Hasta)
  • N/A
  • Updated: [Link]
• Scout interface
  • N/A
  • Updated: [Link]

Validation criteria

Validation criteria to be added to validation report PR: [LINK-TO-VALIDATION-REPORT-PR from the validations repository]

Version specific criteria

• In TGA TN case selectbengal all new ONC fields can be found, optionally excluding ONCCONF which may not have been added to Clinvar yet

In any WGS case: [case-id]

• GC_DROPOUT > 5.00 is set in QC deliverables file
• AT_DROPOUT > 5.00 is set in QC deliverables file

In any WES case: [case-id]

• GC_DROPOUT > 10.00 is set in QC deliverables file
• AT_DROPOUT > 10.00 is set in QC deliverables file

Important

One of the below checkboxes for validation need to be checked

• Added version specific validation criteria to validation report
• Changes validated in standard sections: [validation-section]
• Validation criteria not necessary

Checklist

Important

Ensure that all checkboxes below are ticked before merging.

For Developers

• PR Description
  • Provided a comprehensive description of the PR.
  • Linked relevant user stories or issues to the PR.
• Documentation
  • Verified and updated documentation if necessary.
• Validation criteria
  • Completed the validation criteria section of the template.
• Tests
  • Described and tested the functionality addressed in the PR.
  • Ensured integration of the new code with existing workflows.
  • Confirmed that meaningful unit tests were added for the changes introduced.
  • Checked that the PR has successfully passed all relevant code smells and coverage checks.
• Review
  • Addressed and resolved all the feedback provided during the code review process.
  • Obtained final approval from designated reviewers.

For Reviewers

• Code
  • Code implements the intended features or fixes the reported issue.
  • Code follows the project's coding standards and style guide.
• Documentation
  • Pipeline changes are well-documented in the CHANGELOG and relevant documentation.
• Validation criteria
  • The author has completed the validation criteria section of the template
• Tests
  • The author provided a description of their manual testing, including consideration of edge cases and boundary
    conditions where applicable, with satisfactory results.
• Review
  • Confirmed that the developer has addressed all the comments during the code review.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.45%. Comparing base (7d529e6) to head (2e85b9a).
Report is 50 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1527      +/-   ##
===========================================
- Coverage    99.48%   99.45%   -0.03%     
===========================================
  Files           40       40              
  Lines         1932     2020      +88     
===========================================
+ Hits          1922     2009      +87     
- Misses          10       11       +1     

Flag	Coverage Δ
unittests	99.45% <ø> (-0.03%)	⬇️

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[mathiasbio]

This can be reviewed, I just need to add the validation criteria to the validation report PR!

[fevac]

🚀 LGTM! If there is information about the thresdholds we use in the balsamic documentation you could add some info about these changes. But I don't think that's the case, I think this documentation we keep it in atlas, in which case should also be updated.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud