Question: Can I use ANNOVAR to annotate the bacteria variants?
gravatar for catherine
5.2 years ago by
catherine0 wrote:

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/ 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.

sequencing next-gen • 2.4k views
ADD COMMENTlink modified 5.2 years ago by Istvan Albert ♦♦ 82k • written 5.2 years ago by catherine0
gravatar for Istvan Albert
5.2 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

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:

ADD COMMENTlink written 5.2 years ago by Istvan Albert ♦♦ 82k
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