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to report a little typo
I am new to the GATK forum and I am not sure It's the right place I am posting to so all my apologies if I am in the wrong place. However, I wanted just to report a little typo that occurs here:
Actually, within the usage example box, the "known" argument is written as follow:
Well, if you execute it as it is, it produces the ERROR MESSAGE: Argument with name 'known' isn't defined.
In fact, and according to the same link, for IndelRealigner you should use either --knownAlleles or -known instead of the --known argument which work well for RealignerTargetCreator.
All the best.