arcade

ARCADE — Allelic Recoding via gram-sChmidt for Dominance Effects

C++ tools for identifying compound heterozygotes and encoding biallelic variants for non-additive genetic analysis.

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• Identify compound heterozygotes from phased or unphased genotype data
• Generate gene-level pseudo-variant VCFs for set-based GWAS
• Recode existing VCFs for non-additive or recessive analysis
• Output integrates directly with REGENIE and SAIGE

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Quick links

• Overview -- Background on non-additive genetic effects
• Install -- Docker and source installation
• Documentation -- Full CLI reference for all tools
• Examples -- Runnable workflows with synthetic data
• REGENIE integration -- Variant-level testing with REGENIE
• SAIGE integration -- Set-based burden testing with SAIGE

Citation

If you use arcade in your research, please cite:

Lassen, F.H. et al. (2025). Genome-wide analysis of non-additive genetic effects. (in preparation)

See also the reproducibility repository for scripts accompanying the manuscript.

License

arcade is available under the MIT license.

Source code

Source code is available on Github.

Contact

For bugs and feature requests, please submit an issue on Github.