I annotated my vcf files with SNPs using snpEff which has a pre-built database for the species I work on. But my annotated vcf lacks gene product annotations such as whether a particular gene codes for a hypothetical protein etc.
I tried using snpEff -interval option with a gff3 file with gene product information, but got a error saying unrecognized file type. I also have the same information for my species in a gaf file. But snpEff document says -interval command works with txt,bed.bigbed, vcf and gff.
Can anybody provide me a solution to add these additional information to vcf using snpEff.
Thanks With Best Reagrds Rangi