incorporate indels to gtf/gff file

Question

[grant.hovhannisyan]

Hi Biostars,

I have generated vcf file from RNAseq data and reconstructed alternative haplotype using GATK HaplotypeCaller and FastaAlternateReferenceMaker, respectively. The latter one handles indels, but I am wondering if there any tool that can incorporate indels into the gff/gtf file for that alternative sequence?

Thanks,