shimahm/Ethiopian-Brassica-carinata-oil-traits-GWAS

# Ethiopian Brassica carinata oil traits GWAS: “A reproducible companion repository for the Ethiopian B. carinata oil composition/seed colour GWAS manuscript: data processing, GWAS post-processing, genome functional annotation, haplotype effects, GO enrichment, and key figures.” This repository contains the reproducible analysis workflow for the manuscript: **[Genetic architecture of fatty acid composition, oil content, and seed color in a diverse collection of Ethiopian Brassica carinata]** Shima Mahmoudi et al. It documents all major analysis steps: - phenotype QC + summary statistics - GWAS post-processing and locus definition - Arabidopsis-based functional enrichment of the *B. carinata* genome annotation (RBH + GO transfer) - candidate gene mapping around loci - haplotype (LD-block) effect testing and visualization - GO enrichment analysis for locus candidate genes - generation of manuscript figures and tables > Note: raw sequencing data and restricted-access phenotype files are not redistributed here. This repository provides scripts, metadata, and a reproducible structure for rerunning analyses on authorised systems (HPC/local). --- ## 1) Repository structure This repository is organised to be a lightweight umbrella that points to the code and versions used for the manuscript. It does not duplicate large datasets or every pipeline — instead it pins commits, records run order, and stores final figure-generation scripts and metadata. . ├── 00_project_overview/ │   ├── manuscript_links.md │   ├── data_dictionary.md │   └── analysis_plan.md ├── 01_inputs/ │   ├── phenotype/ # cleaned phenotype tables used in GWAS │   ├── metadata/ # accession / seed colour / altitude metadata │   └── reference/ # pointers (paths) to reference genome + GFF3 ├── 02_genome_annotation/ │   └── README.md # how to reproduce Arabidopsis-transfer annotation ├── 03_gwas_postprocessing/ │   ├── configs/ │   ├── scripts/ │   └── outputs/ ├─ …