I am working on PacBio long read seq data from 10X 3' GEX platform. I have processed hifi_reads.bam with > skera > lima > isoseq and pbmm2 to obtain a mapped.bam file. Now, I would like to call and classify a SNP (chr1:138039992 T/C) in two ways (CD45.1/CD45.2). How would I go about this? So far, I am getting a variants.raw.bcf file from bcftools mpileup. How should I feed this in pigeon classify to make single cell matrix counts?