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Copy-scAT: An R package for detection of large-scale and focal copy number alterations in single-cell chromatin accessibility datasets

The single-cell assay for transposase accessible chromatin (scATAC) is an invaluable asset to profile the epigenomic landscape of heterogeneous cells populations in complex tissue and organ systems. However, the lack of tools that enable the use of scATAC data to discriminate between malignant and non-malignant cells has prevented the widespread application of this technique to clinical tumor samples. Here we describe Copy-scAT, a new computational tool that uses scATAC data to infer both large-scale and focal copy number alterations. Copy-scAT can call both clonal and subclonal copy number changes, allowing identification of cancer cells and cell populations that putatively constitute the tumor microenvironment. Copy-scAT therefore enables downstream chromatin accessibility studies that focus on malignant or non-malignant cell populations in clinical samples that are profiled by scATAC.