So I looked at using the ReadBackedPhasing tool or the Haplotype caller but I already have a calling pipeline setup that works well with my data and I'm really just looking at a way to leverage the vcfs I generate to make consensus fastas of each allele. Sample data is diploid, currently I export to a fasta with ambiguity codes and use dnasp to generate the allele fastas, but I know there's got to be a good way to leverage that vcf information.
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