What is bio-causal-genomics-fine-mapping?

A workflow for fine-mapping, the process of narrowing a GWAS signal to the DNA variants most likely to cause it. GWAS, or genome-wide association study, finds variants linked with a trait but usually cannot identify the causal one by itself.

Use it to analyze GWAS summary statistics or genotype data, account for linkage between variants, and prioritize variants for follow-up experiments.

It helps distinguish a likely causal variant from nearby variants that appear linked because they are often inherited together. It produces probabilities and credible sets, meaning groups of variants that together are expected to contain the causal variant.

bio-causal-genomics-fine-mapping — Skill for Claude Code and Codex by GPTomics: A workflow for fine-mapping, the process of narrowing a…

Install

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.

agentmods

npx agentmods add skills/gptomics/bioskills/fine-mapping

Any agent

npx skills add GPTomics/bioSkills --skill fine-mapping

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/fine-mapping.svg)](https://agentmods.dev/skills/gptomics/bioskills/fine-mapping)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/fine-mapping"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/fine-mapping.svg" alt="Measured on agentmods" height="20"></a>

Per session 161 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 9,565 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. Scan, not verified.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00161	$0.09565
Opus 5	$0.00081	$0.04783
Sonnet 5	$0.00032	$0.01913
Haiku 4.5	$0.00016	$0.00957

Measured 5d ago against content hash d4e7ceb4ea25, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

bio-causal-genomics-fine-mapping 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 5d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (examples/finemap_pipeline.sh, examples/susiex_multiancestry.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-causal-genomics-fine-mapping — 100% identical, 12 lines differ

causal-genomics/fine-mapping/SKILL.md · 436 lines

How it starts

The opening of the file, as written. The whole thing — 436 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: susieR 0.12.27+, coloc 5.2.3+, FINEMAP 1.4.2+, PolyFun (head of omerwe/polyfun 2024), PAINTOR V3.0, SuSiEx (head of getian107/SuSiEx), DAP-G (head of xqwen/dap), pyfocus 0.8+, R 4.3+, PLINK 1.9 / 2.0.

Before using code patterns, verify installed versions match. If versions differ:

R: packageVersion('susieR') then ?susie_rss to confirm argument names (e.g., prior_weights vs prior_variance semantics)
CLI: finemap --help, SuSiEx --help, PAINTOR --help, dap-g --help to confirm flags
Python: polyfun.py --help

If a call throws an error about an argument that no longer exists, introspect the installed function and adapt rather than retrying.

Fine-Mapping

"Narrow my GWAS locus to the variants likely to be causal" -> Fit a sparse Bayesian regression that propagates LD into posterior inclusion probabilities (PIPs) and credible sets, then validate that credible sets correspond to physically reasonable haplotypes given the LD reference.

R (summary statistics + LD): susieR::susie_rss(z, R, n, L=10) + estimate_s_rss LD diagnostic
R (individual-level genotypes): susieR::susie(X, y, L=10)
CLI (shotgun stochastic search): finemap --sss --in-files master.z --n-causal-snps 5 --prob-tol 0.001
CLI (cross-ancestry joint): SuSiEx --sst_file=eur.sst,eas.sst --n_gwas=N1,N2 --ref_file=eur.bim,eas.bim --ld_file=eur_ld,eas_ld --chr_col=1,1 --snp_col=2,2 --bp_col=3,3 --a1_col=4,4 --a2_col=5,5 --eff_col=6,6 --se_col=7,7 --pval_col=8,8 --chr=<chr> --bp=<start,end> --out_dir=<dir> --out_name=<name> (column-number flags and --ld_file are required; populations are assigned by the ORDER of the comma-separated --sst_file/--n_gwas/--ref_file/--ld_file lists, not a --pop flag; see SuSiEx --help)
Python (functional priors): polyfun.py --compute-h2-L2 -> per-SNP priors -> susie_rss with prior_weights=
Python (TWAS fine-mapping): focus finemap on gene-level Z-scores

Read the full file on GitHub · 436 lines

Files

What ships with it

6 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.

Changes

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.

5d ago First seen · 436 lines · 161 tokens per session scan A d4e7ceb4ea25

Subscribe to this mod's changes

bio-causal-genomics-fine-mapping is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 20d ago), licensed MIT. It adds 161 tokens to every session and 9,565 once invoked, about $0.0008 per session on Opus 5. 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 2026-08-30.

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