11 months ago by
There are just now starting to be some tools to sort of do stuff like this. The easiest I've found to use is vartrix, though it doesn't strictly do what you want. It will use a VCF file that you feed it and basically genotype each cell that has coverage for each variant.
Of course, many cells only have one or two (or zero) reads at a given variants, so you can really only say which cells you know have the variant allele - you can't say anything about whether they are hetero/homozygous/wildtype (anything that doesn't have the variant allele is just ambiguous).
It doesn't perform variant calling or clustering based on the SNPs, but it would help you define which cells came from which sample if you have mutation information on each of them.