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I ran the GATK RealignerTargetCreator command and got an output file with some lines in non-interval format (about 6%).
For example: the line chrM:125-346 versus the line chrM:7684
When I ran the next IndelRealigner command it failed with the following error message, indicating the line without interval:
"##### ERROR MESSAGE: Invalid argument value 'targetIntervals' at position 10.
What is the reason for this output? What can I do about it?