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Graph genome

Definition
AI-generated

A graph genome represents multiple haplotypes and structural alleles as a sequence graph—nodes and edges for alternative paths—rather than a single linear reference genome; read mapping and variant calling are performed against this variation graph or equivalent pangenome index.

Topics
Bioinformatics Sequencing and omics tech
Related
Pangenome Read mapping Reference genome

Why it matters in GWAS

Linear references can bias genotyping and obscure variation in diverse cohorts; graph and pangenome references aim to improve imputation, SV genotyping, and association power in polymorphic regions.

Example usage

"Reads were mapped to a human graph genome to reduce reference bias at the HLA locus."

Pangenome Read mapping Reference genome Variation graph
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.
← Gradient Descent Graph Neural Network (GNN) →

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