domains / families / science / genotype-imputation

genotype-imputation

separate

Imputes untyped genotypes against a phased reference panel with Beagle, Minimac4, or IMPUTE5 (array data) or from genotype likelihoods with GLIMPSE2, QUILT2, or STITCH (low-coverage WGS), producing per-variant dosages (DS) with a self-estimated quality (Beagle DR2, Minimac R2, IMPUTE INFO). Covers why the honest output is a dosage posterior not a hard call, why GWAS regresses on DS, why the quality metric is an ESTIMATE of r2 from posterior spread (not validation against truth), the DS/GP/HDS fields, the phasing prerequisite, chunking, chrX ploidy, the Michigan/TOPMed servers (the only access to HRC/TOPMed), and low-coverage WGS as the modern array replacement. Use when increasing variant density for GWAS, harmonizing arrays, inferring untyped variants, or imputing low-coverage sequence. Phase first with haplotype-phasing; prepare the panel with reference-panels; filter with imputation-qc; the GWAS test is population-genetics/association-testing; end-to-end orchestration is workflows/…

When to use

• increasing variant density for GWAS
• harmonizing arrays
• inferring untyped variants
• imputing low-coverage sequence
• array data imputation
• low-coverage WGS imputation

When not to use

• phasing the input
• panel selection and preparation
• quality metrics and filtering thresholds
• GWAS test on dosages
• variant calling
• end-to-end orchestration

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