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
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
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