calling diploid SNVs from long reads
You could try aligning your reads to the draft reference genome with for example minimap2 and calling variants with freebayes. It appears there is a protocol for long reads: https://github.com/ekg/freebayes#re-genotyping-known-variants-and-calling-long-haplotypes

Disclaimer: I have not run freebayes myself, and it may be that this is a terrible idea. I would expect that calling SNVs (Single-nucleotide variants) from PacBio reads is very challenging.  However, with enough coverage, I think it could be possible.