COPILOT is a Containerised wOrkflow for Processing ILlumina genOtyping daTa. The container is deployable on multiple platforms and allows users to quickly and effortlessly prepare, pre-process and understand Illumina microarray SNP data for data analysis through an informative and interactive summary report.
https://khp-informatics.github.io/COPILOT/COPILOT_user_guide.html
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.373