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reference-panels

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Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, HGDP+1kGP/gnomAD, CAAPA), matching panel ancestry to the target, reconciling genome build and chromosome naming, and running the strand/allele harmonization gate. Covers why ancestry-match beats panel size (imputation can only copy haplotypes the panel contains), why palindromic A/T and C/G SNPs flip strand without erroring, why liftover is a strand-flip generator in between-build inverted regions, that HRC is SNP-only and TOPMed is never downloadable (governance can override accuracy), and panel formats (msav, bref3, imp5). Use when choosing a panel for a target ancestry, preparing or converting a panel, aligning study data, or deciding between downloadable and server-only panels. Phasing is haplotype-phasing; imputation is genotype-imputation; PCA for ancestry is population-genetics/population-structure; HLA panels are clinical-databases/hla-typing.

When to use

• choosing a panel for a target ancestry
• preparing or converting a panel
• aligning study data
• deciding between downloadable and server-only panels
• strand/allele harmonization
• build/liftover reconciliation
• format conversion to msav, bref3, or imp5

When not to use

• haplotype-phasing
• genotype-imputation
• population-genetics/population-structure
• clinical-databases/hla-typing
• variant-calling/variant-normalization

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