looking to create IUPAC reference genome

[amythecat]

I am looking for a way to replace the reference allele within a reference genome with the IUPAC code for SNPs of my choosing.

I have been using the FastaAlternateReferenceMaker from GATK to simply switch the reference for the variant allele; however, the application gives an error when I try to switch the allele to a non-nucleotide letter.

Thanks,
Amy

[bmuchmore]

Did you ever find an answer to this?