The demuxlet ‘plp’ option was used to generate a pileup format of 6,145 cells from one well of PBMC 10x data. The reads in the pileup were then modified to reflect the genotypes of individuals sampled from the 1000 Genomes Phase 3 cohort. The pileup was downsampled to obtain different numbers of read-overlapping exonic SNPs (ranging from 5,000 to 100,000) for the whole cohort. To create simulated doublets, we randomly sampled and merged pairs of barcodes within a dataset, resulting in a 5% doublet rate in the original data. For simulations with related individuals, we simulated transcriptomes from 8 individuals in 1000 Genomes with varying degrees of relatedness, ranging from unrelated to parent-child (HG00146, HG00147, HG00500, HG00501, HG00502, HG00512, HG00514, and HG00524).
