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Can I use ANNOVAR to annotate the bacteria variants?

Hi

I am currently working on Leptospira bacteria and would like to annotate the variants that I obtain using ANNOVAR.

My main concern is would it be ok for me to use ANNOVAR to perform this task as most of the examples that I come across in forum and ANNOVAR documentation are on human using hg19.

If yes, how should I fix my code below that I used before when I was working with human cell line in order to annotate the bacteria variants that I have now?

perl ~/annovar/table_annovar.pl \
  first_100.avinput \
  --buildver hg19 \
  --otherinfo \
  ~/annovar/humandb/ \
  --remove \
  -protocol snp135,snp137,snp138,1000g2012apr_all,cg69,esp6500si_all,nci60,cosmic68,refgene \
  --operation f,f,f,f,f,f,f,f,g

Thanks a lot in advance for any reply and comments.

next-gen-sequencing
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updated by Ram Ram • written by catherine • catherine

1 answer

What tools of this type need is a searchable database that they can compare the query data to. Typically these databases are readily available for model organisms and need to be manually created for all others.

The relevant section from the manual is this:

http://www.openbioinformatics.org/annovar/annovar_faq.html#othergenome

• 0 views • link
written by Istvan Albert Istvan Albert

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