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gcatest is a tool to test genome-wide associations (GWAS) with arbitrarily complex population structures. The gcatest algorithm uses a genotype-conditional association test (GCAT), a new method.


Genotype and phenotype; GWAS study


  • Operation: Genotyping
  • Software interface: Command-line user interface; Library
  • Language: ;Association test for genome wide association studies that controls for population structure under a general class of trait. models.;1.4.0;Command-line tool;Library;R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.16.0
  • Credit: National Institute of Health (NIH).
  • Contact: Wei Hao whao _at_, John D. Storey jstorey _at_
  • Collection: Bioconductor


Song M, Hao W, Storey JD "Testing for Genetic Associations in Arbitrarily Structured Populations" Nat Genet. 2015 May;47(5):550-4.
PMID: 25822090
PMCID: PMC4464830

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21.
PMID: 25633503
PMCID: PMC4509590

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.
PMID: 15461798
PMCID: PMC545600

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