/snp-phewas

name: snp-phewas
description: >-
  Variant PheWAS across three curated biobanks, Pan-UK Biobank, FinnGen R12 and the Million
  Veteran Program: one variant in, beta / SE / p / allele frequency for every outcome each
  biobank tested (nulls included), on one effect allele, every untested or unreadable
  outcome kept as a row with a reason, outcomes harmonized across the biobanks, and a
  replication verdict per shared outcome for every biobank pair and across all three.
license: MIT
metadata:
  version: "0.3.0"
  author: Aviv Madar
  domain: genomics
  tags:
    - phewas
    - pan-ukbb
    - finngen
    - million-veteran-program
    - replication
    - summary-statistics
    - tabix
  data_license: >-
    CC-BY-4.0 (Pan-UK Biobank outcome manifest and demo slices); FinnGen R12 public
    results terms, free download with citation and acknowledgment required (FinnGen
    outcome catalog, outcome crosswalk, demo slices); Million Veteran Program summary
    statistics through the NHGRI-EBI GWAS Catalog, EMBL-EBI terms of use with no
    restrictions beyond the data owner's, citation given (MVP outcome catalog and its
    source snapshots, demo slices)
  inputs:
    - name: variant
      type: string
      format:
        - rsid
        - chr_pos_ref_alt
      description: One variant, an rsID (rs12740374) or chr_pos_ref_alt (1_109274968_G_T, GRCh38 unless --build GRCh37), given as --variant or as the first line of an --input text file.
      required: true
  outputs:
    - name: report
      type: file
      format:
        - md
      description: Plain-language report with scope, strongest associations, replication for every biobank pair and all three, what was read, and data citations
    - name: result
      type: file
      format:
        - json
      description: Summary counts, per-dataset status histogram, replication verdict counts per pair and across three, provenance
    - name: rows
      type: file
      format:
        - tsv
      description: One row per catalog outcome per dataset with status and plain-language label
  dependencies:
    python: ">=3.11"
    packages:
      - requests>=2.28
      - matplotlib>=3.7
      - numpy>=1.24
      - pyyaml>=6.0
  demo_data:
    - path: demo/
      description: Real +/-10 kb slices around rs12740374 of 3 Pan-UK Biobank, 3 FinnGen R12 and 2 Million Veteran Program (GWAS Catalog harmonized) outcome files, re-indexed, plus a trimmed FinnGen API answer
  endpoints:
    cli: python skills/snp-phewas/snp_phewas.py --variant {variant} --output {output_dir}
  openclaw:
    requires:
      bins:
        - python3
    always: false
    emoji: "🧭"
    homepage: https://github.com/ClawBio/ClawBio
    os:
      - darwin
      - linux
    install:
      - kind: pip
        package: requests
    trigger_keywords:
      - snp phewas
      - variant phewas across biobanks
      - pan-ukbb phewas
      - finngen phewas
      - million veteran program phewas
      - mvp phewas
      - phewas replication
      - phenome-wide association for rs

🧭 SNP PheWAS (Pan-UK Biobank + FinnGen + Million Veteran Program)

You are **SNP PheWAS**, a specialised ClawBio agent for phenome-wide association lookups. Your role is to read one variant's association with every outcome of three curated biobanks, put them on one effect allele and one outcome key, and say which associations replicate.

Trigger

**Fire this skill when the user says any of:**

• "PheWAS for rs12740374 across UK Biobank, FinnGen and the Million Veteran Program"
• "Does rs12740374 replicate in FinnGen?", "Does it replicate in MVP?"
• "every phenotype this variant was tested for", "all outcomes for this SNP, including nulls"
• "Pan-UKBB PheWAS", "FinnGen PheWAS", "MVP PheWAS", "phenome-wide scan of a variant in biobanks"
• "is this association seen in all three biobanks?", "the same PheWAS in African ancestry"

**Do NOT fire when:**

• The user wants reported associations across the GWAS Catalog / Open Targets credible

sets, eQTLs (GTEx), or BioBank Japan / UKB-TOPMed PheWeb: route to `gwas-lookup`.

• The user wants summary statistics for a REGION (many variants) from one study: route to

`gwas-catalog-region-fetch` or `eqtl-catalogue-region-fetch`.

• The user gives a gene, a disease or a trait rather than a variant: this skill takes one

variant; resolve the variant first.

• The user wants colocalization or Mendelian randomization: route to `mr-region-run` /

`locuscompare-region-render`.

Why This Exists

• **Without it**: a PheWAS lookup is a list of reported associations (significance-selected,

from mixed studies), or one biobank's web page at a time. Nulls are invisible, each source uses its own effect allele, a FinnGen endpoint, a UK Biobank outcome and an MVP phecode for the same disease cannot be lined up, and an outage looks like "no association".

• **With it**: every outcome of each biobank is a row (tested or not, with the reason), on

the Open Targets alternative allele, with FinnGen endpoints, Pan-UK Biobank outcomes and MVP studies on one join key and a verdict per shared outcome for every pair of biobanks and across all three. The default three-biobank read took 159 s and 613 s in two runs with an empty index cache, and 57 s and 66 s with the indexes cached (measured 2026-10-19 on a Mac mini, 16 workers per biobank; the cold spread is the GWAS Catalog's download speed).

• **Why ClawBio**: values are read from the biobanks' own files; nothing is estimated. The

skill `gwas-lookup` calls the same FinnGen web endpoint for its FinnGen leg. This skill differs in five ways: it reads Pan-UK Biobank and the Million Veteran Program (not in `gwas-lookup`); it reads FinnGen's files where the web API hides values (the API reports values only below p = 0.05); it accounts for every outcome with a status; it harmonizes outcomes across the three biobanks; and it calls replication. Use `gwas-lookup` for a fast federated overview first and this skill for the