awk '$3=="gene" || $0 ~/#/{print}' ../04.snp_indel/ref.gff >gene.gff
for query in An1 C24 Cvi Eri Kyo Ler Sha;do
convert2annovar.pl -format vcf4 $query.INV_TRANS.f.vcf -outfile $query.INV_TRANS.input
annotate_variation.pl -regionanno -dbtype gff3 -gff3dbfile gene.gff $query.INV_TRANS.input ./ --buildver unknown --neargene 2000 -out $query.INV_TRANS
done
