Hi,

I’m trying to generate In silico pacbio reads by aligning a shotgun illumina reads to relative reference genome in order to scaffold the illumina shot read library.

I want to make sure the consenus i have incorporates large structural variants and rearrangements. I know GATK’s FastaAlternateReferenceMaker incorporates SNPs and indels but I don’t know if it can do that for the large SVs and rearrangements even if I have them in vcf format. Does any know if it can or know a program that can do that for me?

Thank you!!