I have a Fasta and a VCF of a plant genome, for sequence A and sequence B. Sequence A is the Wildtype, and sequence B is an improved mutated version of it. I have been comparing the variants of the two sequences in IGV, but need to annotate the genes. I have the variants annotated with snpEff, but I need the genes not the variants.
What should I use? I submitted the Fasta to maker, but its taking years, and DAVID doesn't allow VCF or fasta.
Thank you so much for your help!