gbanyan
fe8e13c1a1
Three bugs prevented gnomAD and expression data from contributing to scores: 1. gnomAD COLUMN_VARIANTS mapped "gene" (HGNC symbol) to gene_id instead of gene_symbol, causing JOIN miss with gene_universe (Ensembl IDs) 2. Expression HPA data was fetched but never merged (lf_hpa unused) 3. GTEx versioned Ensembl IDs (ENSG*.5) didn't match gene_universe Results: gnomAD 78.5% coverage, expression 87.4%, 19946 genes with ≥4 layers. HIGH tier refined from 44 → 18 candidates. Validation PASSED (CDH23 96.5th pctl). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
46 lines
894 B
Markdown
46 lines
894 B
Markdown
# Pipeline Reproducibility Report
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**Run ID:** `e7486ff1-f9be-403b-a68d-115fc845f4a1`
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**Timestamp:** 2026-02-15T21:13:12.288563+00:00
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**Pipeline Version:** 0.1.0
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## Parameters
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**Scoring Weights:**
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- gnomAD: 0.20
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- Expression: 0.20
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- Annotation: 0.15
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- Localization: 0.15
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- Animal Model: 0.15
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- Literature: 0.15
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## Data Versions
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- **ensembl_release:** 113
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- **gnomad_version:** v4.1
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- **gtex_version:** v8
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- **hpa_version:** 23.0
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## Software Environment
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- **python:** 3.14.3
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- **polars:** 1.38.1
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- **duckdb:** 1.4.4
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## Filtering Steps
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| Step | Input Count | Output Count | Criteria |
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|------|-------------|--------------|----------|
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| load_scored_genes | 0 | 0 | |
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| apply_tier_classification | 0 | 0 | |
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| write_candidate_output | 0 | 0 | |
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| generate_visualizations | 0 | 0 | |
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## Tier Statistics
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- **Total Candidates:** 21103
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- **HIGH:** 18
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- **MEDIUM:** 9577
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- **LOW:** 11508
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