Files

gbanyan e2a3dc2bc8 fix: rescue gnomAD genes with non-Ensembl IDs via gene_symbol fallback

gnomAD v4.1 gene_id column is mixed: ~101K Ensembl IDs + ~111K NCBI numeric.
Now falls back to gene_symbol → gene_universe lookup for non-ENSG entries.

Coverage: 78.5% → 90.3% (17,875 → 20,555 genes with gnomAD scores).
Sufficient evidence (≥4 layers): 19,946 → 20,683 genes.
Validation median percentile: 79.9% → 81.1%.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-02-16 05:49:27 +08:00

894 B

Raw Blame History

Pipeline Reproducibility Report

Run ID: 093b405b-5a20-4f35-b5b8-04f02451789d Timestamp: 2026-02-15T21:49:14.940206+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: 21177
HIGH: 82
MEDIUM: 9626
LOW: 11469

894 B Raw Blame History

Pipeline Reproducibility Report

Parameters

Data Versions

Software Environment

Filtering Steps

Tier Statistics

894 B

Raw Blame History