Hi all,

I'm trying to annotate resequenced maize genome - other than reference B73.

I know how to apply variants from VCF file ( using either bcftools or vcf-consensus) -> create non-reference genome fasta file. Now I'm trying to make custom gtf file for further analyses (variants caused of course that coordinates changed). I suppose there are way to modify reference gtf/gff file, but I've searched the web and haven't find out how to do it.

I'm suprised, because resequencing is probably one of the most popular application of NGS.

I think it would be much simpler and wiser using existing information for reference line rather than using tools like MAKER or so... Even if it is not 100% correct (variants could for example destroy TSS site).

What do you think, any hints/tips/directions would be appreciated.