PLINK Basics

What it does

PLINK Basics documents practical CLI patterns to convert between VCF, BED/BIM/FAM, PED/MAP and the newer PLINK2 formats, plus standard quality-control pipelines. It provides concrete command snippets for format conversion, allele frequency checks, missingness statistics, sex checks, and combined QC steps used commonly in population genetics workflows.

When to use it

Use this skill when preparing genotype data for downstream analysis (GWAS, PCA, association testing), when needing reliable format conversions, or when performing sample/variant QC. It's intended for bioinformaticians and computational biologists working with large genotype datasets who need tested PLINK command examples.

What's included

• Scripts: none included, SKILL.md contains extensive CLI examples.
• References: usage-guide and example files present in repo sibling files.
• Instructions: step-by-step command blocks for VCF→PLINK, PLINK→VCF, MAF/genotype/missingness/HWE filters, sample/variant selection, sex checks, and merging datasets. The file also outlines interpretation of outputs and practical thresholds.

Compatible agents

Best used with CLI-capable agents or automation that can run shell commands (GitHub Actions, local shells, or agent frameworks that expose a plink binary).