GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs).


OSCA (OmicS-data-based Complex trait Analysis) is a sister tool of GCTA, developed for estimating the proportion of phenotypic variance captured by all DNA methylation (DNAm) probes, LMM-based methylome-wide association analysis, or methylation QTL mapping.


SMR is a software tool that implements the SMR & HEIDI methods to test for pleiotropic association between the expression level of a gene and a complex trait of interest using summary-level data from GWAS and expression quantitative trait loci (eQTL) studies (Zhu et al. 2016 Nature Genetics).