I want to figure out how I can identify SNP's in a single-cell RNA-sequencing run produced by the 10x Genomics Chromium Single Cell 3' Solution. I want to essentially cluster cells into groups by their SNPs to see if differences can be detected in donor versus host cells. What is the best way to go about this process and is there anywhere I can find an established workflow for this?
I wanted to do something similar to snpclust: https://github.com/10XGenomics/single-cell-3prime-snp-clustering but it seems like it is not supported.
Any help would be appreciated.
Thank you in advance!