bio-population-genetics-plink-basics
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.
npx skills add BioTender-max/awesome-bio-agent-skills --skill plink-basics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # PLINK Basics **"Convert my VCF to PLINK format and run QC"** → Handle PLINK file format conversions (VCF, BED/BIM/FAM, PED/MAP) and apply standard genotype QC filters for MAF, genotyping rate, and HWE. - CLI: `plink2 --vcf input.vcf --make-bed` for format conversion - CLI: `plink2 --maf 0.01 --geno 0.05 --hwe 1e-6` for QC filtering File formats, conversion, and quality control filtering with PLINK 1.9 and 2.0. ## File Formats ### 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` | Binar
- Version Compatibility
- File Formats
- Binary Format (Recommended)
- PLINK 2.0 Format
- Text Format (Legacy)
- Format Conversion
- VCF to PLINK Binary
- PLINK Binary to VCF
- PED/MAP to Binary (PLINK 1.9 Only)
- Binary to PED/MAP
- PLINK 1.9 to 2.0 Format
- Quality Control Filtering
- MAF Filter (Minor Allele Frequency)
- Genotyping Rate Filters
PLINK 1.9 plink --vcf input.vcf.gz --make-bed --out output PLINK 2.0 plink2 --vcf input.vcf.gz --make-bed --out output With sample ID handling plink2 --vcf input.vcf.gz --double-id --make-bed --out output plink --bfile input --recode vcf --out output plink2 --bfile input --export vcf --out output Compressed VCF plink2 --bfile input --export vcf bgz --out output
What does the bio-population-genetics-plink-basics skill do?
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill plink-basics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.