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feat: stratification of VAFs #68

Merged
merged 41 commits into from
May 17, 2024
Merged

feat: stratification of VAFs #68

merged 41 commits into from
May 17, 2024

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johanneskoester
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containing just todos

@famosab
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famosab commented Apr 12, 2024 •
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More things need to be solved:

  • Truth VCF has to be handed to calc_precision_recall.py
  • Arrays need to be defined in constructor (Classification)
  • Correct VAF record needs to be accessed (sample name?)
  • Handle cases where VAF is denoted in INFO field
  • (Change implementation to be more efficient)
  • VAF stratification has to be used in report

@famosab
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famosab commented Apr 19, 2024

We found that rtg vcfeval removes INFO and FORMAT fields.

johanneskoester
johanneskoester commented Apr 22, 2024
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Great work!

workflow/scripts/calc-precision-recall.py Outdated Show resolved Hide resolved
workflow/resources/datavzrd/precision-recall-config.yte.yaml Outdated Show resolved Hide resolved
workflow/resources/datavzrd/precision-recall-config.yte.yaml Show resolved Hide resolved
@johanneskoester johanneskoester merged commit 8d2c121 into main May 17, 2024
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@johanneskoester johanneskoester deleted the feat/vaf-stratification branch May 17, 2024 20:07
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Fantastic!

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@johanneskoester @famosab @BiancaStoecker