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Add simple SV filtration filter presets and adjust defaults #616

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holtgrewe opened this issue Aug 25, 2022 · 1 comment · Fixed by #618
Closed

Add simple SV filtration filter presets and adjust defaults #616

holtgrewe opened this issue Aug 25, 2022 · 1 comment · Fixed by #618
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enhancement New feature or request

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@holtgrewe
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holtgrewe commented Aug 25, 2022

Is your feature request related to a problem? Please describe.
There are a lot of presets in the SV variant calling that are hard to use. Further, the defaults are not stringent enough.

Describe the solution you'd like
Add bootstrap dropdowns to allow for the following quick presets:

  • Frequency:
    • all: clear all max carriers/allele thresholds
    • relaxed:
      • DGV: 20
      • DGV Gold Standard: 10
      • dbVar: 40
      • ExAC: 20
      • 1000 Genomes: 10
      • gnomAD-SV: 10
      • in-house background: 10
    • strict:
      • DGV: 10
      • DGV Gold Standard: 5
      • dbVar: 20
      • ExAC: 10
      • 1000 Genomes: 5
      • gnomAD-SV: 5
      • in-house background: 5

Variants & Effects:

  • all: select all, clear size
  • relaxed: select all, min SV size: 500
  • CNV only: only DEL/DUP

Quality:

  • all
  • relaxed
    • min PR var: 1
    • min SR var: 1
    • min SR+PR var: 4
  • strict
    • min PR var: 1
    • min SR var: 1
    • min SR+PR var: 10

Also, adjust the default values to be

  • Frequency max carriers/alleles: relaxed
  • Variants & Effects: relaxed
  • Quality: relaxed

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 added this to the bollonaster-2.0.0 (dev) milestone Aug 25, 2022
@holtgrewe holtgrewe self-assigned this Aug 25, 2022
@holtgrewe
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Resolution Proposal
This can be implemented in the front-end alone. No adjustment to server code is necessary.

Affected Components
VarFish server

Affected Modules/Files
svs/templates/...

Required Architectural Changes
None

Required Database Changes
None

Backport Possible?
No

Resolution Sketch

  • add HTML with the dropdowns
  • write JavaScript to adjust the defaults

holtgrewe added a commit that referenced this issue Aug 25, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Aug 25, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Aug 25, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Aug 25, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Aug 26, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Aug 29, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Sep 6, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Sep 6, 2022
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
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