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.
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-Falcão 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. https://doi.org/10.1038/ncomms10532
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