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IndelRealigner known resources
Would you please let us know how "IndelRealigner" makes use of "known" resources? I assume it already has the intervals of interest for realignment from the "RealignerTargetCreator". So it's not clear why it needs the resources again. Would it use them for making any sort of decision to reject or accept realigned indels?
Also, please let us know what happens (algorithmically) if we don't provide the same resources used in "RealignerTargetCreator" to the program.