GWAS PRS¶

Calculate polygenic risk scores (PRS) from 23andMe or AncestryDNA data using curated PGS Catalog scores. Supports trait-based lookup or direct PGS ID specification for diseases such as type 2 diabetes, coronary artery disease, and breast cancer.

Quick Demo¶

python3 skills/gwas-prs/gwas_prs.py \
  --demo \
  --output /tmp/prs_demo

CLI Reference¶

# Score by trait name
python3 skills/gwas-prs/gwas_prs.py \
  --input <23andme_file> \
  --trait "type 2 diabetes" \
  --output <report_dir>

# Score by PGS Catalog ID
python3 skills/gwas-prs/gwas_prs.py \
  --input <23andme_file> \
  --pgs-id PGS000013 \
  --output <report_dir>

# Demo mode
python3 skills/gwas-prs/gwas_prs.py \
  --demo \
  --output /tmp/prs_demo

Argument	Required	Description
`--input`	Yes*	Path to 23andMe or AncestryDNA raw data file
`--trait`	No	Trait name for PGS Catalog lookup
`--pgs-id`	No	Direct PGS Catalog score ID
`--output`	Yes	Output directory for report and figures
`--demo`	No	Run with synthetic demo patient (~300 SNPs, 6 traits)

*Not required when using --demo.

Output¶

report.md -- PRS report with risk percentiles and population context
figures/ -- Risk distribution plots per trait
tables/ -- Per-SNP effect allele contributions (CSV)
commands.sh -- Reproducibility script
checksums.sha256 -- Output verification