Workflow of MitoSort

A. Schematic showing the purpose of MitoSort. B. Overview of MitoSort pipeline. Firstly, mitochondrial reads are realigned and putative SNPs are called. Subsequently, count matrices of reference and alternative alleles are generated for each cell, where each row represents a cell and each column represents a variant. Following that, sample-specific germline variants are identified for each individual. Cross-genotype doublets are then detected by a beta-binomial model. Lastly, singlets are demultiplexed for downstream analyses. SNP, single-nucleotide polymorphism; mtDNA, mitochondrial DNA; mtRNA, mitochondrial RNA; mtscATAC-seq, mitochondrial single-cell assay for transposase-accessible chromatin with sequencing; ASAP-seq, ATAC with select antigen profiling by sequencing; GMM, Gaussian Mixture Model.