Variant calling in nonmodel organisms with snpArcher.

snpArcher pipeline produces high-quality, analysis-ready variant callsets from raw sequencing data in non-model organisms, demonstrated with 137 burrowing owl genomes.

• Why it matters: Reliable variant calling in non-model species is hindered by complex workflows and lack of species-specific best practices, limiting population genomic insights.
• What they did: A six-phase Snakemake-based protocol was developed, guiding users through installation, sample setup, execution, quality control, and downstream filtering, with an interactive QC dashboard.
• The result: Applying the protocol improved demographic inference accuracy by removing artifacts like low-coverage samples and sex-linked regions, enabling reproducible, robust population analyses.