bio-phasing-imputation-haplotype-phasing

npx skills add majiayu000/claude-skill-registry --skill haplotype-phasing-gptomics-bioskills --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Haplotype Phasing ## 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 \ map=genetic_map.txt \ nthreads=8 \ window=40 \ overlap=4 \ ne=20000 \ # Effective population size seed=12345 # For reproducibility ``` ## Phase Per Chromosome ```bash # Process each chromosome separately for chr in {1..22}; do java -Xmx16g -jar beagle.jar \ gt=input.chr${chr}.vcf.gz \ map=genetic_maps/plink.chr${chr}.GRCh38.map \ out=phased.chr${chr} \ nthreads=8 done # Concatenate chromosomes bcftools concat phased.chr*.vcf.gz -Oz -o phased.all.vcf.gz bcftools index phased.all.vcf.gz ``` ## SHAPEIT5 Phasing (for Large Datasets) ```bash # Phase common variants first shapeit5_phase_common \ --input input.vcf.gz \ --map genetic_map.txt \ --output phased_common.bcf \ --thread 8 \ --

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 chromosomes