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BaseRecalibrator help is misleading (gatk 184.108.40.206)
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.