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I got errors when ran GATK RealignerTargetCreator and IndelRealigner in v2.4.9. I've checked many related discussions and comments. First, I got an error like "we encountered an extremely high quality score of 69" with option -S LENIENT and the GATK program stalled. So I added "--fix_misencoded_quality_scores", and then I got different error message "ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '0'" now. I tried older versions of GATK and both java 1.6 and 1.7. I'm hoping that you can help this. Please let me know if I'm missing something. Thanks!
Giltae Song, Ph.D.
Department of Genetics
School of Medicine