Concepts¶
These pages cover the design decisions, trade-offs, and biology behind snpArcher. None of this is required to use the pipeline, but it will help you make better choices for your project.
- Pipeline architecture: How the pipeline is structured and why.
- Variant calling: GATK vs. bcftools vs. DeepVariant, and when to choose each.
- Parallelization: The scatter-by-Ns strategy.
- QC metrics: What each QC figure means biologically.
- Filtering philosophy: SFS-guided filtering with rationale and worked example.
- Non-model organisms: Challenges specific to non-model organisms and how snpArcher addresses them.