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gbanyan fe8e13c1a1 fix: restore gnomAD and expression evidence layers for complete 6-layer scoring

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>

2026-02-16 05:25:37 +08:00

894 B

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Pipeline Reproducibility Report

Run ID: e7486ff1-f9be-403b-a68d-115fc845f4a1 Timestamp: 2026-02-15T21:13:12.288563+00:00 Pipeline Version: 0.1.0

Parameters

Scoring Weights:

gnomAD: 0.20
Expression: 0.20
Annotation: 0.15
Localization: 0.15
Animal Model: 0.15
Literature: 0.15

Data Versions

ensembl_release: 113
gnomad_version: v4.1
gtex_version: v8
hpa_version: 23.0

Software Environment

python: 3.14.3
polars: 1.38.1
duckdb: 1.4.4

Filtering Steps

Step	Input Count	Output Count	Criteria
load_scored_genes	0	0
apply_tier_classification	0	0
write_candidate_output	0	0
generate_visualizations	0	0

Tier Statistics

Total Candidates: 21103
HIGH: 18
MEDIUM: 9577
LOW: 11508

894 B Raw Blame History

Pipeline Reproducibility Report

Parameters

Data Versions

Software Environment

Filtering Steps

Tier Statistics

894 B

Raw Blame History