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 GWAS data.
SMR is a software tool that implements the SMR & HEIDI methods to test for pleiotropic association between a molecular phenotype (e.g., gene expression level) and a complex trait of interest using summary-level data from GWAS and xQTL studies.
GSMR is A R-package which implements the GSMR (Generalised Summary-data-based Mendelian Randomisation) method to test for putative causal association between a risk factor and a disease using GWAS summary statistics.
OSCA (OmicS-data-based Complex trait Analysis) is a sister tool of GCTA, developed for estimating the proportion of phenotypic variance captured by genome-wide measures of a molecular phenotype (e.g., all DNA methylation probes), LMM-based omics-wide association analysis, and xQTL mapping analysis, etc.
DENTIST (Detecting Errors iN analyses of summary staTISTics) is a quality control tool for GWAS summary data. It can detect errors in either the GWAS or LD reference data and heterogeneity between the GWAS and LD reference samples.