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.
THISTLE (testing for heterogeneity between isoform-eQTL effects) is a transcript-based splicing QTL (sQTL) mapping method that uses either individual-level genotype and RNA-seq data or summary-level isoform-eQTL data.