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Genome-wide Complex Trait Analysis (GCTA)

Definition
AI-generated

GCTA is a command-line software package for genome-wide complex trait analysis.

Topics
Post-GWAS
URL
https://yanglab.westlake.edu.cn/software/gcta/
Related
Conditional Association Analysis Genetic Relationship Matrix (GRM) Genome-Wide Association Study (GWAS)

Why it matters in GWAS

GCTA is one of the standard tools for moving from single-variant association results to variance-component and locus-level follow-up analyses. Its file formats, GRM conventions, and GREML outputs appear frequently in methods sections and tutorial pipelines.

Example usage

"We used GCTA to build the GRM from LD-pruned SNPs and estimate SNP heritability with GREML."

Conditional Association Analysis Genetic Relationship Matrix (GRM) Genome-Wide Association Study (GWAS) Genome-based Restricted Maximum Likelihood (GREML) Linear Mixed Model (LMM) Principal Component Analysis (PCA) SNP Heritability
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

  • Yang J, et al. (2011). GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. https://doi.org/10.1016/j.ajhg.2010.11.011
  • GWASTutorial: GCTA-GREML.
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