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I am running RealignerTargetCreator using GATK version GenomeAnalysisTK-1.2-4-gd9ea764 and I am getting the following error:
I already checked that I am using the right Reference FASTA file and the correct .bam file, that I have used for alignment before. Therefore, I am clueless why I am getting this error?
I would appreciate your help regarding this problem. Any suggestion is welcome?