cellsnp-lite

cellsnp-lite is an efficient tool for genotyping single cells. cellsnp-lite was initially designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference. Now besides RNA-seq data, cellsnp-lite could also be applied on DNA-seq and ATAC-seq data, either in bulk or single-cell.