Input files reads and reference have incompatible contigs while Running GATK:RealignerTargetCreator
I am running RealignerTargetCreator using GATK version GenomeAnalysisTK-1.2-4-gd9ea764 and I am getting the following error:
ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = scaffold69676_size1796 / 3149
ERROR contig reference = scaffold69676_size1796 / 1758.
ERROR reads contigs = [scaffold1_size320545, scaffold2_size291774, scaffold3_size284740..........`
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?