GWAS Summary Statistics QC Starter

Use this skill to run a deterministic local pass over GWAS summary statistics, flag common QC issues, and emit a compact interpretation plan for downstream clumping, heritability, and functional follow-up.

What This Skill Does

• reads a GWAS summary-statistics table with common header aliases
• standardizes core fields such as chromosome, position, alleles, effect size, p-value, sample size, EAF, and INFO
• flags malformed rows, low-information variants, duplicate variant identifiers, and ambiguous palindromic SNPs
• writes a flagged TSV plus a JSON summary with top hits and recommended downstream tools

When To Use It

• when you need a reusable starter for gwas beyond a notes-only frontier placeholder
• when a dataset needs fast summary-statistics QC before LDSC, fine-mapping, PRS, or interpretation work
• when you want a stable local contract that does not depend on large reference panels or remote services

Run

python3 skills/genomics/gwas-starter/scripts/run_gwas_summary_qc.py \
  --input skills/genomics/gwas-starter/examples/toy_sumstats.tsv \
  --config skills/genomics/gwas-starter/examples/qc_config.json \
  --out-tsv scratch/gwas/gwas_qc.tsv \
  --summary-out scratch/gwas/gwas_qc_summary.json

Notes

• The starter is intentionally local and deterministic. It surfaces issues that should be resolved before genome-wide downstream tools consume the file.
• Header normalization supports common aliases such as CHR, BP, EA, NEA, BETA, OR, P, N, EAF, and INFO.
• For allele harmonization against reference genomes, SSF export, or LD-based follow-up, read refs.md and use the cited canonical tools.