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@bencap bencap commented Nov 17, 2025

This pull request introduces a new analysis script for MaveDB that counts unique variant effect measurements falling within ACMG-classified functional ranges. The script provides summary statistics on the clinical interpretability of variant effect data using ACMG evidence strength frameworks. It is a read-only script intended for data analysis and reporting.

New ACMG classification analysis script:

  • Added calibrated_variant_effects.py script to src/mavedb/scripts/, which analyzes MaveDB score sets to count variants with functional scores in ACMG-classified calibration ranges, providing summary statistics on classification coverage.
  • Implements logic to:
    • Filter out superseded and private score sets, and require calibrations.
    • Identify ACMG-classified functional ranges based on the presence of ACMG criteria, evidence strength, or points.
    • Count unique variants with non-null scores that fall within ACMG-classified ranges, ensuring each variant is counted only once per score set.
    • Report per-score-set and overall summary statistics, including the number of score sets with ACMG classifications, total unique variants processed, number of classified variants, and covered target genes.
  • Provides a CLI interface using click, with options for dry-run and commit modes (though the script is read-only).

@bencap bencap requested a review from sallybg November 17, 2025 18:34
@bencap bencap linked an issue Nov 17, 2025 that may be closed by this pull request
@bencap bencap merged commit dee025c into release-2025.5.1 Nov 24, 2025
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@bencap bencap deleted the feature/bencap/586/script-for-calibration-variant-effect-figures branch November 24, 2025 19:52
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Calibration only statistics calculation

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