bio-phasing-imputation-haplotype-phasing
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.
npx skills add BioTender-max/awesome-bio-agent-skills --skill haplotype-phasing --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+ Before using code patterns, verify installed versions match. If versions differ: - 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. # Haplotype Phasing **"Phase my genotypes into haplotypes"** → Resolve which alleles are inherited together on each chromosome for downstream imputation, HLA typing, or population genetic analyses. - CLI: `java -jar beagle.jar gt=input.vcf out=phased` (Beagle 5.4) - CLI: `shapeit4 --input input.vcf --output phased.vcf` (SHAPEIT) ## Beagle 5.4 Phasing (Recommended) ```bash # Download Beagle 5.4 wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar # Basic phasing java -jar beagle.22Jul22.46e.jar \ gt=input.vcf.gz \ out=phased # Output: phased.vcf.gz (phased genotypes) # With genetic map (improves accuracy) java -jar beagle.22Jul22.46e.jar \ gt=input.vcf.gz \ map=plink.chr22.GRCh38.map \ out=phased ``` ## Beagle Options ```bash java -jar beagle.22Jul22.46e.jar \ gt=input.vcf.gz \ out=phased \ m
- Version Compatibility
- Beagle 5.4 Phasing (Recommended)
- Beagle Options
- Phase Per Chromosome
- SHAPEIT5 Phasing (for Large Datasets)
- SHAPEIT5 with Reference Panel
- Beagle with Reference Panel
- Input Preparation
- Check Phasing Results
- Genetic Maps
- Key Parameters
- Memory Requirements
- Phasing Accuracy Metrics
- Related Skills
Download Beagle 5.4
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar
Basic phasing
java -jar beagle.22Jul22.46e.jar \
With genetic map (improves accuracy)
Process each chromosome separately
for chr in {1..22}; do
java -Xmx16g -jar beagle.jar \
done
Concatenate chromosomesWhat does the bio-phasing-imputation-haplotype-phasing skill do?
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill haplotype-phasing --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.