Hello, I'm trying to generate new reference annatoation file(GTF) of sub-population (or ecotype). Currently, I have reference genome annotation file(GTF) and vcf file from the sub-population. but I am now afraid using current reference genome annotation file(GTF) becuse indels would ruine the orignal coordinates of GTF.
So Is there any tools for shift orginal GTF coordinate base on VCF ?
Thank you very much!