bio-phasing-imputation-haplotype-phasing - Phase Genotypes into Haplotypes for Imputation
Infers haplotype phase from population linkage disequilibrium using SHAPEIT5, SHAPEIT4, Eagle2, or Beagle for imputation and phase-dependent analyses.
Tags
Updated: 2026-10-02Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Estimate haplotype phase
- Phase common variants
- Phase rare variants
- Ligate phased chunks
- Benchmark switch errors
- Handle pedigree phasing
Inputs
- Unphased genotypes
- Genetic map
- Reference panel
- Genome build
- Pedigree data
Outputs
- Phased haplotypes
- Phased BCF or VCF
- Switch-error metrics
Requirements
- SHAPEIT5, Eagle2, or Beagle
- Build-matched genetic map
- Compatible reference panel
- Version-verified CLI