bio-phasing-imputation-genotype-imputation
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill genotype-imputation --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+, 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. # Genotype Imputation **"Impute missing genotypes using a reference panel"** → Fill in untyped variants by leveraging LD patterns from a reference panel to increase variant density for GWAS or cross-platform harmonization. - CLI: `java -jar beagle.jar gt=input.vcf ref=panel.vcf out=imputed` - CLI: `minimac4 --refHaps panel.m3vcf --haps input.vcf --prefix imputed` ## Beagle Imputation ```bash # Basic imputation java -jar beagle.jar \ gt=study.vcf.gz \ ref=reference_panel.vcf.gz \ map=genetic_map.txt \ out=imputed # Output: imputed.vcf.gz with imputed genotypes ``` ## Beagle with Options ```bash java -Xmx32g -jar beagle.jar \ gt=study.vcf.gz \ ref=reference_panel.vcf.gz \ map=genetic_map.txt \ out=imputed \ nthreads=8 \ gp=
- Version Compatibility
- Beagle Imputation
- Beagle with Options
- Impute Per Chromosome
- IMPUTE5 (Alternative)
- Minimac4 (Michigan Imputation Server)
- Input Preparation
- Extract Imputation Quality
- Output Formats
- Using Dosages for GWAS
- Quality Thresholds
- Key Parameters
- Imputation Servers
- Related Skills
Basic imputation
java -jar beagle.jar \
java -Xmx32g -jar beagle.jar \
for chr in {1..22}; do
done
Concatenate
bcftools concat imputed.chr*.vcf.gz -Oz -o imputed.all.vcf.gz
bcftools index imputed.all.vcf.gz
Newer IMPUTE software
impute5 \What does the bio-phasing-imputation-genotype-imputation skill do?
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill genotype-imputation --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.