Question: Bacterial genome annotation using annovar
gravatar for Sondes Kalboussi
2.1 years ago by
Sondes Kalboussi0 wrote:

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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Sondes Kalboussi0

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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Medhat8.4k

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

Perl {}/ --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

ADD REPLYlink written 2.0 years ago by Sondes Kalboussi0
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