Bacterial genome annotation using annovar

Question

[Sondes Kalboussi]

Hello, am writing my own pipeline in python in order to annotate bacterial genome MTB, am new in this field and am a bit lost , I converted my VCF to appropriate annovar input format, then i got stack, i have to use dbSNP to annotate SNP and hrv37 as the reference genome for annotation but dont really know the correct command format or what i really need to provide more. I read the manual but it is not really helping me. Anyone with experience in using Annovar to annotate bacterial genomes? Thanks in advance

[Medhat]

I am assuming that you read this manual , to be able to get help here; you need first to try and write down what did you do and what error/s or where exactly you stumble.

[Sondes Kalboussi]

Thanks for the clarification, actually i still preparing the files that i would need to run table_annovar.pl, my output must have gene location and gene function annotation so am using the followin g command

Perl {}/table_annovar.pl --vcfinput {} {} --outfile {} --buildver H37RV --nastring . --protocol refGene,dbsnp --operation g,r,f --vcfinput""".format(self.annovar,input_vcf,MTBdb)

Am a bit lost cause am not sure if the databases am using are correct ones for gene location and gene function annotation