I know some of my past posts haven't made too much sense, so I hope this makes sense.
I have a .gff file with the annotations for the entire genome of my plant species, and I want to use it to annotate just the chloroplast genome. How do I extract or apply just that part of the .gff file to my chloroplast files(formatted as a VCF and .bam files). Is it possible to use IGV and my .gff file to annotate my VCF and bam files? (of my organisms genome mapped against the chloroplast genome).
Thank you so much in advance!!