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Display "disease" gene flag in SV results #620

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holtgrewe opened this issue Aug 25, 2022 · 1 comment · Fixed by #621
Closed

Display "disease" gene flag in SV results #620

holtgrewe opened this issue Aug 25, 2022 · 1 comment · Fixed by #621
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@holtgrewe
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enhancement New feature or request
Milestone
bollonaster-2.0.0...

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@holtgrewe
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Is your feature request related to a problem? Please describe.
The small variant results display a flag if a gene is a known disease gene. This information is very useful and missing for structural variants.

Describe the solution you'd like
Add such an icon to the SV result display.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe added the enhancement New feature or request label Aug 25, 2022
@holtgrewe holtgrewe self-assigned this Aug 25, 2022
@holtgrewe holtgrewe added this to the bollonaster-2.0.0 (dev) milestone Aug 25, 2022
@holtgrewe
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Resolution Proposal
Join the disease gene model to the SV gene effect annotation as is done for small variants.

Affected Components
VarFish Server

Affected Modules/Files

  • variants.queries
  • svs.queries
  • svs.views

Required Architectural Changes
None

Required Database Changes
None

Backport Possible?
Not desired

Resolution Sketch

  • adjust variants.queries to allow re-use of ExtendQueryPartsDiseaseGeneJoin
  • adjust svs module to use this and display it in the results

holtgrewe added a commit that referenced this issue Aug 25, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
fb15a57 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
@holtgrewe holtgrewe linked a pull request Aug 25, 2022 that will close this issue
620 display disease gene flag in sv results #621
Merged
holtgrewe added a commit that referenced this issue Aug 25, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
2573163 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 25, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
1b850e6 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#620).
5b4faa7 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
f90dbd4 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#620).
f46a2e6 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#620).
e119393 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#620).
35b523c 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#620).
e671bbb 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
7056603 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 29, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
93e5de9 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
da83488 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Sep 6, 2022
@holtgrewe
Displaying disease gene icon also for SVs (#620).
d0e4fe4 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
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@holtgrewe holtgrewe

Labels
enhancement New feature or request
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Milestone
bollonaster-2.0.0 (dev)
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Successfully merging a pull request may close this issue.

620 display disease gene flag in sv results varfish-org/varfish-server
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@holtgrewe