Gapit

Gapit, short for Genome Association and Prediction Integrated Tool, is a software package for statistical genetics designed to perform genome-wide association studies (GWAS) and genomic prediction on large genotype and phenotype datasets. It is widely used in plant and animal genetics to identify marker–trait associations and to predict breeding values.

Gapit is implemented as an R package that provides a suite of tools for GWAS analyses, including standard linear models and mixed linear models, as well as more flexible multi-locus approaches and genomic prediction methods. It supports correction for population structure through principal components and kinship matrices, handles large data sets, and includes visualization utilities such as Manhattan plots and Q-Q plots, along with facilities to export results.

Gapit originated in the statistical genetics community in the early 2010s and has since been maintained with additional methods and documentation. It is commonly employed in crop genetics and breeding programs to map quantitative trait loci and to estimate genomic estimated breeding values.

Gapit is distributed as open-source software for R, with documentation and tutorials available from its project repository and associated websites. It is cross-platform and designed to integrate with standard R workflows for data import, analysis, and visualization.