305-high-quality-SV-dataset-of-3KRGP

The R pipelines (BWGS) and bash workflows for rice genomic analysis. Three marker strategies are supported:variant_calling: Stand‑alone bash scripts for variant discovery (SNP/INDEL with GATK; SV with Delly)SNP: SNP‑only GS workflowsSV: SV‑only GS workflows (raw / genic / intergenic)Both: Combined SNP + SV GS workflowsEach sub‑folder contains:One or more core R scripts (BWGS_with_*.R) that run 5‑fold × 10‑repeat cross‑validation on up to ten GS models (GBLUP, RF, EGBLUP, RR, BRR, LASSO, EN, BL, BB, RKHS).Shell wrappers (run_*.sh) that set the working directory and call the corresponding R script for a specific GWAS filtering threshold (p < 0.05 / 0.01 / 0.001 or “whole” set).The scripts and pipelines for the study are also accessible in github.com/lianglunping/305-high-quality-SV-dataset-of-3KRGP/tree/main.