AlphaGenome Variant Effect Pipeline

A batch pipeline for multi-modal variant effect prediction using AlphaGenome. Given a CSV of variants, the script predicts the effect of each variant on RNA-seq, chromatin accessibility (ATAC), CTCF binding, and histone modification (H3K27ac) in a specified cell type, and saves a figure for each variant.

---

Requirements

• Python 3.10+
• AlphaGenome package and a valid API key (request access here)
• Dependencies: alphagenome

---

Input CSV Format

Prepare a CSV file with the following required columns:

Note: The gene_name and rsID values in the example CSV may not be accurate, they are placeholder examples for testing the code only. Please replace them with your actual variants before running.

gene_name	rsID	chr	position	ref_allele	alt_allele
TBK1	rs149000064	chr12	64488488	GAATT	G
TP53	rs28934578	chr17	7674220	G	A

• position: 1-based genomic coordinate (hg38)
• ref_allele / alt_allele: can be SNVs or indels
• Any extra columns in the CSV are safely ignored

A template CSV (variants_input.csv) is included in this repository.

---

Usage

python ./PATH_to_code/alphagenome_variant_pipeline.py \
    --csv variants_input.csv \
    --output_dir ./alphagenome/figures \
    --ontology EFO:0001187 \
    --api_key YOUR_API_KEY

Code Running:

Output directory : ./alphagenome
Run timestamp    : 2026-02-28 18:29:06
Loaded 4 variant(s) from /dfs7/swaruplab/zechuas/Collaborations/alphagenome/Test/autopiepline/variants_input.csv

Initializing AlphaGenome model...
Loading GTF annotation (this may take a moment on first run)...
Annotation loaded.

============================================================
Processing: TBK1 | rs149000064 | chr12:64488488:GAATT>G
============================================================
============================================================
  Variant : TBK1 | rs149000064 | chr12:64488488:GAATT>G
  Ontology: EFO:0001187
────────────────────────────────────────────────────────────
  RNA-seq (+) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq (-) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq poly-A                   3 track(s)   EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq
    → 3 identical tracks found — averaging as true replicates
    → Track: EFO:0001187 polyA plus RNA-seq
  ATAC                             1 track(s)   EFO:0001187 ATAC-seq
  CHIP-TF (CTCF)                   2 track(s)   EFO:0001187 TF ChIP-seq CTCF, EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF
    [WARNING] 2 different tracks found — selecting wildtype/unmodified:
      - EFO:0001187 TF ChIP-seq CTCF  [wildtype]
      - EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF  [MODIFIED - skipped]
    → Selected: EFO:0001187 TF ChIP-seq CTCF
  CHIP-Histone (H3K27ac)           1 track(s)   EFO:0001187 Histone ChIP-seq H3K27ac
────────────────────────────────────────────────────────────

Quantification saved:
  → Gene level: ./alphagenome/TBK1_rs149000064_EFO_0001187_summary.csv
Saved: ./alphagenome/TBK1_rs149000064_EFO_0001187_variant_effect.png

============================================================
Processing: TP53 | rs28934578 | chr17:7674220:G>A
============================================================
============================================================
  Variant : TP53 | rs28934578 | chr17:7674220:G>A
  Ontology: EFO:0001187
────────────────────────────────────────────────────────────
  RNA-seq (+) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq (-) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq poly-A                   3 track(s)   EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq
    → 3 identical tracks found — averaging as true replicates
    → Track: EFO:0001187 polyA plus RNA-seq
  ATAC                             1 track(s)   EFO:0001187 ATAC-seq
  CHIP-TF (CTCF)                   2 track(s)   EFO:0001187 TF ChIP-seq CTCF, EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF
    [WARNING] 2 different tracks found — selecting wildtype/unmodified:
      - EFO:0001187 TF ChIP-seq CTCF  [wildtype]
      - EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF  [MODIFIED - skipped]
    → Selected: EFO:0001187 TF ChIP-seq CTCF
  CHIP-Histone (H3K27ac)           1 track(s)   EFO:0001187 Histone ChIP-seq H3K27ac
────────────────────────────────────────────────────────────

Quantification saved:
  → Gene level: ./alphagenome/TP53_rs28934578_EFO_0001187_summary.csv
Saved: ./alphagenome/TP53_rs28934578_EFO_0001187_variant_effect.png

============================================================
Processing: BRCA1 | rs80357713 | chr17:43071077:A>T
============================================================
============================================================
  Variant : BRCA1 | rs80357713 | chr17:43071077:A>T
  Ontology: EFO:0001187
────────────────────────────────────────────────────────────
  RNA-seq (+) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq (-) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq poly-A                   3 track(s)   EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq
    → 3 identical tracks found — averaging as true replicates
    → Track: EFO:0001187 polyA plus RNA-seq
  ATAC                             1 track(s)   EFO:0001187 ATAC-seq
  CHIP-TF (CTCF)                   2 track(s)   EFO:0001187 TF ChIP-seq CTCF, EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF
    [WARNING] 2 different tracks found — selecting wildtype/unmodified:
      - EFO:0001187 TF ChIP-seq CTCF  [wildtype]
      - EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF  [MODIFIED - skipped]
    → Selected: EFO:0001187 TF ChIP-seq CTCF
  CHIP-Histone (H3K27ac)           1 track(s)   EFO:0001187 Histone ChIP-seq H3K27ac
────────────────────────────────────────────────────────────

Quantification saved:
  → Gene level: ./alphagenome/BRCA1_rs80357713_EFO_0001187_summary.csv
Saved: ./alphagenome/BRCA1_rs80357713_EFO_0001187_variant_effect.png

============================================================
Processing: APOE | rs429358 | chr19:44908684:T>C
============================================================
============================================================
  Variant : APOE | rs429358 | chr19:44908684:T>C
  Ontology: EFO:0001187
────────────────────────────────────────────────────────────
  RNA-seq (+) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq (-) total                1 track(s)   EFO:0001187 total RNA-seq
  RNA-seq poly-A                   3 track(s)   EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq, EFO:0001187 polyA plus RNA-seq
    → 3 identical tracks found — averaging as true replicates
    → Track: EFO:0001187 polyA plus RNA-seq
  ATAC                             1 track(s)   EFO:0001187 ATAC-seq
  CHIP-TF (CTCF)                   2 track(s)   EFO:0001187 TF ChIP-seq CTCF, EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF
    [WARNING] 2 different tracks found — selecting wildtype/unmodified:
      - EFO:0001187 TF ChIP-seq CTCF  [wildtype]
      - EFO:0001187 TF ChIP-seq CTCF genetically modified (insertion) using CRISPR targeting H. sapiens CTCF  [MODIFIED - skipped]
    → Selected: EFO:0001187 TF ChIP-seq CTCF
  CHIP-Histone (H3K27ac)           1 track(s)   EFO:0001187 Histone ChIP-seq H3K27ac
────────────────────────────────────────────────────────────

Quantification saved:
  → Gene level: ./alphagenome/APOE_rs429358_EFO_0001187_summary.csv
Saved: ./alphagenome/APOE_rs429358_EFO_0001187_variant_effect.png

Track summary saved : ./alphagenome/track_summary_20260228_182906.txt

============================================================
PIPELINE COMPLETE  [2026-02-28 18:29:06]
  Success       : 4
  Errors        : 0
  Figures       : ./alphagenome
  Track summary : ./alphagenome/track_summary_20260228_182906.txt
  Run summary   : ./alphagenome/pipeline_summary_20260228_182906.csv

All Arguments

Argument	Required	Default	Description
--csv	✅	—	Path to input CSV file
--output_dir	✅	—	Directory to save output figures
--api_key	✅	—	Your AlphaGenome API key
--ontology	✅	EFO:0001187	Cell type ontology term (default: HepG2/Liver)
--interval_size	❌	1048576	Model input context window in bp (1 Mb). The model needs this large window for accurate predictions — only change if you have a specific reason
--zoom	❌	32768	Region displayed in the output figure in bp (32 kb). Does not affect prediction accuracy

---

Output

For each variant, the pipeline saves:

• A .png figure named {gene_name}_{rsID}_{ontology}_variant_effect.png showing REF vs ALT tracks for all modalities
• A track_summary_{timestamp}.txt logging the tracks available for each variant, which track was selected, and any warnings (e.g. CRISPR-modified tracks that were skipped)
• A pipeline_summary_{timestamp}.csv listing the status (success/error) of each variant

All output files are timestamped so multiple runs never overwrite each other.

Example figure for TBK1:

各位老师欢迎提出意见 More than happy to make changes