How-to guides¶
How-to guides are goal-oriented recipes. Each one answers a specific "How do I…?" question. They assume you have a working snpArcher installation and basic command-line familiarity.
| Guide | Goal |
|---|---|
| Install snpArcher | Get snpArcher, Snakemake, and conda/mamba set up |
| Create a sample sheet | Build the CSV that tells snpArcher about your samples |
| Configure your run | Set up config.yaml for your dataset |
| Run locally | Execute on a workstation |
| Run on HPC | Execute on SLURM or other schedulers |
| Interpret QC reports | Read the interactive QC dashboard |
| Filter and postprocess | Filter your VCF by samples, sites, and callable regions |
| Add a custom module | Extend snpArcher with your own Snakemake module |
| Troubleshoot errors | Fix common problems |