Entering edit mode
6.7 years ago
grant.hovhannisyan
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2.6k
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,