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.