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.