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GLIMPSE2

Definition
AI-generated

GLIMPSE2 is a genotype imputation method tailored for ultra-low-coverage whole-genome sequencing: it phases and imputes from genotype likelihoods using large reference panels, aiming to recover genome-wide variation cost-effectively at scale.

Topics
GWAS
Related
Coverage Haplotype Genotype Imputation

Why it matters in GWAS

As biobanks adopt low-pass WGS strategies, specialized imputation (rather than array-only or standard high-coverage pipelines) affects power, QC, and comparability with array-imputed GWAS; GLIMPSE2 is representative of this workflow class.

Example usage

"We imputed 1× WGS with GLIMPSE2 against the same TOPMed-based reference used for array imputation to compare call sets."

Coverage Haplotype Genotype Imputation Imputation Reference Panel Low-Pass Sequencing Haplotype Phasing Whole-Genome Sequencing (WGS)
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Rubinacci S, et al. (2023). Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. Nat Genet.
  • Sun Q, Li Y. (2026). Advances in haplotype phasing and genotype imputation. Nat Rev Genet. https://doi.org/10.1038/s41576-025-00895-2
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