I am working with bam files for single-cell RNA sequencing data that have barcodes under the tag -XX and UMIs under the tag -SS. However, I am trying to use this bam file as input into multiple variant-calling workflows (freebayes+vartrix, cellsnp-lite, etc.), but am running into issues, as the outputs of all of these are empty and don't contain variants. I know these workflows work with bam files outputted by Cellranger, and am wondering if this is an issue with the way my Bam file is formatted. Since Cellraner uses the -CB tag for barcodes, how can I change my -XX to by -CB? Or is there another workaround?