I have scRNA-seq data where I have sequenced each individual separately and then all pooled together. I'm interested in turning these standalone samples into a genetic reference, but I'm not sure how to go about that. I can imagine I could run vireo with N=2 or 3 and expect convergence/maximization of the ELBO when assigning >95% of the cells to a single identity, but that sounds janky and could pick up heterogeneity coming from different cell types displaying different SNPs. Is there a more vireo-friendly way to do this?
I have scRNA-seq data where I have sequenced each individual separately and then all pooled together. I'm interested in turning these standalone samples into a genetic reference, but I'm not sure how to go about that. I can imagine I could run vireo with N=2 or 3 and expect convergence/maximization of the ELBO when assigning >95% of the cells to a single identity, but that sounds janky and could pick up heterogeneity coming from different cell types displaying different SNPs. Is there a more vireo-friendly way to do this?