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Input files known and reference have incompatible contigs
I have a question. I use the GATK RealignerTargetCreator, I have this error message.
ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig known = chrM / 16569
ERROR contig reference = chrM / 16571.
there are many questions about this, but there isn't definite answer.