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Chain File

Definition
AI-generated

A chain file stores pairwise whole-genome alignment blocks between assemblies and is used to map coordinates from one reference build to another.

Topics
Bioinformatics Formats
URL
https://genome.ucsc.edu/goldenPath/help/chain.html
Related
Genome Coordinate System Liftover Variant

Why it matters in GWAS

GWAS summary statistics and variant annotations are often produced on different genome builds, so chain files are essential for consistent coordinate harmonization before meta-analysis and interpretation.

Example usage

"We used the hg19-to-hg38 chain file to liftover summary statistics before cross-cohort meta-analysis."

Genome Coordinate System Liftover Variant
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

  • UCSC Genome Browser. Chain Format. https://genome.ucsc.edu/goldenPath/help/chain.html
← Utah Residents with Northern and Western European Ancestry (CEU) Chain-of-Thought (CoT) →

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