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Update nallo rank model #117

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Update nallo rank model #117

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@fellen31 fellen31 commented Dec 11, 2025 •
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Description

Closes #93

Added

  • REVEL, dbnsfp_gerp++_rs, dbnsfp_phastcons100way_vertebrate, dbnsfp_phylop100way_vertebrate for SNVs
  • most severe pli for SVs

Changed

  • Not reported score for SVs from +4 to +6, to align with short-read
  • gnomAD SNVs to same frequencies and scores to same as in short-read
  • CoLorsDB and LoqusDB SVs to same frequencies as short-read SV databases, except set common to 5% (from 10%)
  • +3 score to not_reported SV model, basically rendering SVs models not used in ranking
  • Feature truncation score to align with short-read

How to prepare for test

  • Ssh to relevant server (depending on type of change)
  • Use stage: us
  • Paxa the environment: paxa
  • Install on stage (example for Hasta): 
    bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

  • Do ...

Expected test outcome

  • Check that ...
  • Take a screenshot and attach or copy/paste the output.

Review

  • Tests executed by
  • "Merge and deploy" approved by
    Thanks for filling in who performed the code review and the test!

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

  • Document in ...
  • Deploy this branch on ...
  • Inform to ...

@fellen31
Update database frequencies
b8d8323 
+3 regardless of model

Add polyphen, revel, sift, dbnsfp_gerp++_rs, dbnsfp_phastcons100way_vertebrate, dbnsfp_phylop100way_vertebrate

Add most severe pli for SVs

update rank model suggestion
@fellen31
remove sift and polyphen until we know how it works
d4052a7
@fellen31
update feature truncation to align with short read
f06d4ce
@fellen31 fellen31 marked this pull request as ready for review December 11, 2025 15:39
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Update feature_truncation in Nallo rank model?

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@fellen31