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Can I use the fasta alternate reference maker to make a reference genome containing IUPAC codes?
I have been using the fasta alternate reference maker to switch the reference and variant alleles in the human reference genome. I would like to use it to change the reference allele to the IUPAC ambiguity code instead, but I get an error when I include anything but A, G, C, or T as the variant allele in my vcf file. Is there a way to work around this with the fasta alternate reference maker?