Hello Team,
I am trying to run
java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I header.bam -o realigned.intervals
my reference is a trinity assembled genome with GO terms in fasta header already indexed . What error I keep getting is :
Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '13
Any idea what is going wrong ?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If you search the forum you'll see that people have reported this happening when the files have been generated or edited on a windows machine, iirc. You'll need to edit the file to correct any encoding errors.

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