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Variation graph

Definition
AI-generated

A variation graph (sequence graph) encodes reference and alternate alleles as shared and branching paths, generalizing a linear genome; tools build indexes from it for alignment, genotyping, and pangenome analysis.

Topics
Bioinformatics
Related
Assembly graph Graph genome Pangenome

Why it matters in GWAS

Representing known variation in the reference structure can reduce allelic bias in mapping and variant discovery, supporting more uniform GWAS quality across ancestries as graph references mature.

Example usage

"The pipeline genotyped SVs by aligning to a chromosome-scale variation graph built from haplotype assemblies."

Assembly graph Graph genome Pangenome Reference genome
Related-term network

Click any node to open that term page.

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

  • Garrison E, et al. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference structure. Nat Biotechnol.
← Variant Quality Score Recalibration (VQSR) Variational Autoencoder (VAE) →

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