RealignerTargetCreator - lines without interval
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Hello, 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.

ERROR Invalid argument value 'GRC13283077_var_list' at position 11."

What is the reason for this output? What can I do about it? Please advice.

Thanks, Lily

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