Step 2 : Demultiplexing samples

The MRD product and pipeline allows multiplexing of up to three patient samples in the same Tapestri run. The demultiplexing algorithm leverages germline SNP genotypes to label each cell according to which patient it originated from. The customer must provide known germline SNP genotypes for each patient via a multi-sample VCF file, which can be acquired via bulk sequencing. The pipeline will fail if there are < 5 germline SNPs provided, and emits a warning if there are < 10.  The algorithm constructs a database of the germline SNPs, including the expected genotype profile for cell doublets. Each cell is then assigned to the best-matching patient or cell doublet using a likelihood-based score. The final two steps in the pipeline remove poor quality cells to avoid false patient assignments: (i) filter out cells where < 30% of the germline SNPs are genotyped, and (ii) filter out cells if the number of genotype discrepancies between the best matched patient is ≥ 10 or if the percentage is ≥ 30%.