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Old 08-21-2012, 06:42 AM   #1
amythecat
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Location: Columbus, OH

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Default looking to create IUPAC reference genome

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
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Old 06-12-2013, 11:42 PM   #2
bmuchmore
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Did you ever find an answer to this?
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