Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill gwas-startergit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/gwas-starter)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/gwas-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/gwas-starter.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00000 | $0.00397 |
| Opus 5 | $0.00000 | $0.00198 |
| Sonnet 5 | $0.00000 | $0.00079 |
| Haiku 4.5 | $0.00000 | $0.00040 |
Grade A, and why
gwas-starter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
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
gwasbeyond 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, andINFO. - For allele harmonization against reference genomes, SSF export, or LD-based follow-up, read
refs.mdand use the cited canonical tools.
What ships with it
12 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- assets/README.md 121 B
- assets/toy_gwas_qc_summary.json 2.4 KB
- assets/toy_gwas_qc.tsv 642 B
- examples/qc_config.json 308 B
- examples/README.md 317 B
- examples/resource_context.json 803 B
- examples/toy_sumstats.tsv 389 B
- metadata.yaml 1.7 KB
- refs.md 1.7 KB
- scripts/run_frontier_starter.py 2.4 KB runs code
- scripts/run_gwas_summary_qc.py 14 KB runs code
- tests/test_gwas_starter.py 4.4 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago First seen · 33 lines · 0 tokens per session scan A 9663ed6ae7fc
gwas-starter is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It costs nothing until one of its globs matches a file; then it loads 397 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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