VarsGT: Rice Graph Pangenome Index and Test Datasets

This dataset provides reference resources and test files for VarsGT (Variants Genotyping), a workflow designed to genotype second-generation sequencing (NGS) reads against predefined variant panels, including marker panels derived from rice cohorts and user-provided custom panels. The dataset primarily includes the Nip-42rice_GraphPangenome_Index, a prebuilt rice graph pangenome index used for graph-based read alignment, along with example test files for demonstrating and validating the VarsGT workflow. By integrating allele-based genotyping strategies, VarsGT determines the genotypes of SNPs, INDELs, and structural variants (SVs) at sites represented in the selected variant panel and generates standardized VCF files for downstream analyses, particularly genomic selection. These resources are provided to facilitate the deployment, testing, and reproducible application of VarsGT in rice genomic research.