Table 3.

Summary of GWAS-related functions in PLINK, GEMMA, FarmCPU_pkg, and rMVP

Function	Item	Software
		PLINK	GEMMA	FarmCPU_pkg	rMVP
Input	Hapmap	×	×	√	√
	VCF	√	×	×	√
	Binary	√	√	×	√
	Numeric	×	×	√	√
	BIMBAM	×	√	×	×
	Quality control	√	×	×	×
Model	GLM	√	√	√	√
	MLM	×	√	×	√
	FarmCPU	×	×	√	√
Population structure	PCs	√	×	√	√
	GRM	×	√	×	√
Variance component estimation	Brent	×	×	×	√
	EMMAX	×	×	√	√
	Fast-LMM	×	×	√	√
	HE regression	×	√	×	√
Output	P value, SE, effect	√	√	√	√
	Manhattan plot	×	×	√	√
	Q-Q plot	×	×	√	√
	SNP density plot	×	×	×	√
	Phenotype distribution	×	×	×	√
	PCA plot	×	×	√	√

Note: √, software with related functions; ×, software without related functions. MLM, mixed linear model; FarmCPU, fixed and random model circulating probability unification; PC, principal component; GRM, genomic relationship matrix; EMMAX, Efficient Mixed-Model Association eXpedited; FaST-LMM, Factored Spectrally Transformed Linear Mixed Models; HE regression, Haseman-Elston regression; SE, standard error; Q-Q plot, Quantile-Quantile plot; PCA, principal component analysis.