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Error while calling variants in Inflenza virus

Hello GATK team,

I am trying to call variants in haploid Influenza virus. I took unaligned reads obtained by mapping to the virus host genome. The unaligned reads were then mapped to the virus reference using BWA.The bam obtained was used for variant calling. When I use RealignerTargetCreator I get the following error:

ERROR MESSAGE:Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '45'

I created .dict and fai files for the reference genome also.

I am not sure what this error means since all the required files for my reference has been created. Is there anything I am missing?

Could you help me out here.

Thank you in advance.


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