This release (v1.0) provides the code and scripts used to process and analyze ddRAD sequencing data from 15 Indian vulture samples, and to produce the figures and tables in the associated manuscript. Included files bash/ — ordered pipeline scripts for trimming, mapping, joint genotyping, filtering, LD pruning, FST and diversity calculations. R/ — plotting and summary-stat scripts (PCA, FST heatmaps, π, Tajima's D, RoH, heterozygosity, mutation-load). python/ — helper scripts and dadi pipeline. environment.yml — suggested conda environment (see README for manual install notes). Purpose & reproducibility This snapshot is provided for reproducibility: the numeric prefixes in scripts/ indicate recommended execution order. Large raw sequencing files are not included here. How to cite After Zenodo archives this release a DOI will be available. Suggested citation format: Shukla, M. (2026). Indian Vulture Population Genomics (ddRAD-data processing and analysis) (Version v1.0) [code]. Zenodo. DOI: Notes Inspect and edit absolute paths in scripts before running. Some packages (e.g., admixture) may require manual installation — see README for instructions.