creation of custom database in ANNOVAR for plant genome

Question

[Sathish]

Hi everyone,

How to create a custom database in ANNOVAR for plant genome (draft genome) using GFF3 file?

I have downloaded corresponding genomic sequences and their gff3 file. Then gff3 file was used to annovar readable format by using the following command.

$ gff3ToGenePred pgonome.gff3 pgenome

Any body could post the steps to proceed next step..

Note: I have a VCF file with detected number of SNP's.