phasing-imputation

You can phase genotypes and impute missing variants from VCF data by providing your genotype file, sample metadata, and a matched reference panel to generate haplotype-resolved genotypes and imputation QC metrics.

Haplotype phasing resolves genotypes into maternal and paternal haplotypes, while imputation fills missing variants using a reference panel, producing ancestry-aware data suitable for downstream association studies.

Yes, a suitable reference panel is required for genotype imputation and haplotype phasing. It enables ancestry-aware matching and provides the haplotype context needed to impute missing variants with confidence.

Yes, the workflow uses Python-based tooling with wrappers for phasing and imputation engines, plus bcftools and pandas for VCF data handling and processing sample metadata to generate imputed genotype sets.

To generate imputation QC metrics, run imputation using a matched reference panel and sample metadata; the workflow outputs imputation QC metrics alongside imputed genotype sets to assess confidence for association studies.

Yes, phasing-imputation supports ancestry-aware phasing, reference-panel matching, and QC-driven analyses across both array and sequencing variants, producing phased genotypes and imputed variants for downstream use.