SNP annotation

[baika]

Hi
What is the best and easy way of annotating SNPs/InDels if reference genome of the organism is not available through UCSC genome browser? I have a list of SNPs and InDels generated using BWA-GATK in VCF format from the bacteria Staphylococcus aureus. I am trying to annotate them (location of these SNPs in context of reference genome) using ANNOVAR. I have converted this VCF file into the annovar format using convert2annovar.pl option, and it looks fine.

In order to make my own annotation database I created gff3 file of the reference genome (GenBank file) using bp_genbank2gff3.pl BioPerl script and also validated it using an online gff3 validator available at http://modencode.oicr.on.ca/cgi-bin/...te_gff3_online. The gff3 file looks perfect. Please suggest how to use this gff file for annotation in ANNOVAR.

Thanks

[sytiger]

I would like to know too.

Any one could give a hint?

Thanks