feat: add SOR filter to WGS TN

[mathiasbio]

Description

As observed in deviation https://github.com/Clinical-Genomics/Deviations/issues/719 we sometimes have an issue with strandbias in the WGS TN workflow. The cause of these variants with excessive strandbias is unknown but variants with 100% strandbias as these variants had, should never have been maintained in the final clinical VCF.

Issue in balsamic: #1505

Added

• SOR filter to WGS TN SNV quality filter

Changed

• [Description]

Fixed

• [Description]

Removed

• [Description]

Documentation

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

Tests

Feature Tests

• Test rerun case from deviation and see that the problematic strandbias variants are removed
• Investigate the change in the number of variants for at least 4 TN cases before and after this filter

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: [Link]
• 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 [Justification].
  • 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]

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.
• 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.
• 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.

[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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.49%. Comparing base (7d529e6) to head (6763f28).
Report is 36 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1506      +/-   ##
===========================================
+ Coverage    99.48%   99.49%   +0.01%     
===========================================
  Files           40       40              
  Lines         1932     1991      +59     
===========================================
+ Hits          1922     1981      +59     
  Misses          10       10              

Flag	Coverage Δ
unittests	99.49% <ø> (+0.01%)	⬆️

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