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 infromation into the vcf file??