Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-population-genetics-plink-basics

Maintainer FreedomIntelligence · Last updated April 1, 2026

PLINK2 for GWAS QC, LD pruning, and basic population genetics.

OpenClawNanoClawAnalysisReproductionbio-population-genetics-plink-basics🧠 bioos extended suitebioos extended bioinformatics suiteplink2

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-population-genetics-plink-basics

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

File formats, conversion, and quality control filtering with PLINK 1.9 and 2.0.
plink --vcf input.vcf.gz --make-bed --out output.

Source Doc

Excerpt From SKILL.md

Binary Format (Recommended)

File	Contents
`.bed`	Binary genotype data
`.bim`	Variant information (chr, ID, cM, pos, A1, A2)
`.fam`	Sample information (FID, IID, father, mother, sex, pheno)

PLINK 2.0 Format

File	Contents
`.pgen`	Binary genotype data (compressed)
`.pvar`	Variant information
`.psam`	Sample information

Text Format (Legacy)

File	Contents
`.ped`	Genotypes (FID, IID, father, mother, sex, pheno, genotypes)
`.map`	Variant positions (chr, ID, cM, pos)

Use cases

Use bio-population-genetics-plink-basics for genomics and bioinformatics workflows.
Apply bio-population-genetics-plink-basics to sequencing, variant, or omics analysis tasks.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

association-testing - GWAS with filtered data
population-structure - PCA after QC
variant-calling/vcf-basics - VCF format before conversion

Related skills

Back to directory

Data & ReproBioinformatics & Genomics

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproBioinformatics & Genomics

alpha-vantage

Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.

Claude CodeAnalysis

K-Dense-AI/claude-scientific-skillsView

Data & ReproBioinformatics & Genomics

bio-alignment-filtering

Filter alignments by flag, quality, region, or paired status.

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproBioinformatics & Genomics

bio-alignment-indexing

Index BAM/CRAM files with samtools index for random access.

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView