incorporate indels to gtf/gff file · Biostar

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incorporate indels to gtf/gff file

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,

rna-seq vcf haplotype indels

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written 9.0 years ago by grant.hovhannisyan

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