bio-population-genetics-scikit-allel-analysis
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structures. Use when analyzing population genetics in Python.
npx skills add BioTender-max/awesome-bio-agent-skills --skill scikit-allel-analysis --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: bcftools 1.19+, matplotlib 3.8+, numpy 1.26+ 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. # scikit-allel Analysis **"Analyze population genetics in Python"** → Read VCF files into efficient array structures, compute allele frequencies, diversity statistics, PCA, and selection scans using scikit-allel. - Python: `allel.read_vcf()`, `allel.GenotypeArray()`, `allel.mean_pairwise_difference()` Python library for population genetics analysis with efficient array data structures. ## Installation ```bash pip install scikit-allel # Optional: zarr for chunked storage pip install zarr ``` ## Reading VCF Files ### Load VCF ```python import allel callset = allel.read_vcf('data.vcf.gz') print(callset.keys()) # dict_keys(['samples', 'calldata/GT', 'variants/CHROM', 'variants/POS', 'variants/REF', 'variants/
- Version Compatibility
- Installation
- Reading VCF Files
- Load VCF
- Specify Fields
- Large Files (Chunked)
- Genotype Arrays
- GenotypeArray
- Basic Operations
- Missing Data
- Allele Counts and Frequencies
- By Population
- Haplotype Arrays
- PCA
pip install scikit-allel pip install zarr
What does the bio-population-genetics-scikit-allel-analysis skill do?
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structures. Use when analyzing population genetics in Python.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill scikit-allel-analysis --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.