iPat

iPat performs genome-wide association studies (GWAS) and genomic prediction/genomic selection (GS) to associate genotypes with phenotypes and enable phenotype prediction.

Key Features:

• GWAS and GS support: Performs genome-wide association studies (GWAS) and genomic prediction/genomic selection (GS) analyses.
• Third-party package integration: Integrates models implemented in GAPIT, PLINK, FarmCPU, BLINK, rrBLUP, and BGLR for analytical workflows.
• File format handling: Accepts any input data format and performs automatic file conversions for selected downstream packages.
• GWAS-assisted genomic prediction: Implements a GWAS-assisted genomic prediction method that enables genomic prediction using GWAS methods such as FarmCPU.

Scientific Applications:

• Association mapping: Identification of genotype–phenotype associations through GWAS.
• Phenotype prediction: Predicting phenotypes from genotypes via genomic prediction/selection for breeding and research.
• Translational applications: Application of GWAS-assisted genomic prediction to molecular breeding and medical genomics for trait selection and risk prediction.

Methodology:

Integration of third-party CLI packages (GAPIT, PLINK, FarmCPU, BLINK, rrBLUP, BGLR), automatic file format conversion, and implementation of a GWAS-assisted genomic prediction method enabling use of GWAS methods (e.g., FarmCPU) for genomic prediction.