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.