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GWAS Pipeline

GWAS Pipeline

GWAS Pipeline is a pipeline tool for genome-wide association analysis (GWAS). The GWAS pipeline can filter, create a kinship matrix, covariate files, run EMMAX, computes Manhattan and QQ plots. The GWAS has functions for computing a summary of the most significant SNPs with calculated allele effects. Requirements: Python v2.6-v2.7, NumPy, Plink v1.9, and R.


GWAS study


  • Operation: Analysis, Sequence analysis, Genetic variation analysis
  • Input: PLINK formatted
  • Output: -
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: 6.4
  • Maturity: Mature
  • Credit: -
  • Contact: srm4 _at_
  • Collection: -


McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, Branchini DA, Kuser-Falc√£o PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J "Open access resources for genome-wide association mapping in rice" Nat Commun. 2016 Feb 4;7:10532.
PMID: 26842267
PMCID: PMC4742900

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