plink2-gwas-analysis SKILL.md skillA
plink2-gwas-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/plink2-gwas-analysis@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/variant/plink2-gwas-analysis/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 14,248 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), IBD estimation, PCA, and linear/logistic regression GWAS. Outputs Manhattan-ready summary stats. Use regenie or SAIGE for biobanks (>100k samples) needing mixed models.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PLINK2 — GWAS and Population Genetics ## Overview PLINK2 is the high-performance successor to PLINK 1.9, designed for genome-wide association studies (GWAS) and population genetics analysis on large cohorts. It processes genotype data in PLINK binary format (.bed/.bim/.fam), VCF, and BGEN formats — performing sample and variant quality control (QC), kinship estimation, principal component analysis (PCA), and linear/logistic regression association testing. PLINK2 is 10–100× faster than PLINK 1.9 on most tasks due to multithreading and optimized I/O. Output files are compatible with downstream visualization (Manhattan/QQ plots) and meta-analysis tools. ## When to Use - Running GWAS on a case-control or quantitative trait cohort after genotyping array QC - Performing sample QC: missingness, heterozygosity outliers, sex check, cryptic relatedness - Computing genome-wide LD pruning for PCA or relatedness estimation - Running PCA on genotype data to identify population stratification - Converting between PLINK binary, VCF, and BGEN formats - Filtering variants by MAF, HWE, missingness, or INFO score in VCF/imputed data …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/plink2-gwas-analysis@sha256:b29121ca6b11663dThe line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_yjc5cgwzyiqghw7c)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 14,248 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 14,297 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 12,350 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 12,755 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14248 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yjc5cgwzyiqghw7c GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/plink2-gwas-analysis GET https://markdownregistry.com/api/v1/blob/b29121ca6b11663df507223679531af75225bba56b6f2587cd2ded6489785502
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.