Application for haploid organisms with mixed strains/clones per sample - with 10x single cell isoSeq data

[JesseRop]

Dear Developers,

Thank you very much for this great tool. Just went through the paper and it very cool work!
I work on plasmodium parasites and have sc-isoseq data (generated on 10X then sequenced on pac bio to get long reads). I have different strains (with different genotypes) in my sample and would like to call SNPs for these and if possible search for sQTLs. Do you know if I can use your tool for this and how i'd go about it.
I look forward to your response!