BaseRecalibrator help is misleading (gatk 4.0.12.0)

I was trying to use the BaseRecalibrator walker. The help says:

Required Arguments:

--input,-I:String             BAM/SAM/CRAM file containing reads  This argument must be specified at least once.
                              Required. 

--known-sites:FeatureInput    One or more databases of known polymorphic sites used to exclude regions around known
                              polymorphisms from analysis.  This argument must be specified at least once. Required. 

--output,-O:File              The output recalibration table file to create  Required. 

--reference,-R:String         Reference sequence file  Required. 

However, if I include the ":" into the command line, for example with "--known-sites:#####", I get errors such as:

A USER ERROR has occurred: No value found for tagged argument: known-sites:#####

While if I replace the ":" with a space, such as "--known-sites #####", everything works.

It seems to me like after updating the command line format in GATK4, someone forgot to update the help text. I felt this was quite disruptive. I actually think that the right way to do it would have been to provide instructions in the error message explaining that ":" need to be removed in GATK4. This would go a long way to make a smooth transition experience for users moving from GATK3 to GATK4.

Answers

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