Thank you for making this wonderful tool. I have used this pipeline on six samples and was surprised to see very few somatic variants after all the filtering. I noticed that in a substantial number of cases, the reason the filtering failed was because the expected cell type and observed cell type were different.
Even though you have tried to answer similar questions elsewhere, do you think you could explain how computing the genotypes for each cell at variant sites works? Also, what does it mean for all the cells of a particular cell type have mismatches in the expected cell type and observed cell type columns? Does this point towards there being some issue with the cell type annotation quality?
Thank you for making this wonderful tool. I have used this pipeline on six samples and was surprised to see very few somatic variants after all the filtering. I noticed that in a substantial number of cases, the reason the filtering failed was because the expected cell type and observed cell type were different. Even though you have tried to answer similar questions elsewhere, do you think you could explain how computing the genotypes for each cell at variant sites works? Also, what does it mean for all the cells of a particular cell type have mismatches in the expected cell type and observed cell type columns? Does this point towards there being some issue with the cell type annotation quality?