Ion torrent Bam to Annotation

Question

[alok.helix]

I sequenced a bacterial genome using Ion Torrent machine and I assembled the reads against a reference genome (closely related to the sequenced Bacteria). Now I have the bam file. I plan on using Prokka to annotate my data. I believe Prokka doesnot take in a bam file for annotation purpose. What should I do further? Should I extract a consensus sequence from the bam file? If so How should I proceed and if wrong, how will I proceed? Also how to get gene information into the vcf file?

https://github.com/tseemann/prokka/blob/master/README.md#invoking-prokka