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 ?