Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
BaseRecalibrator help is misleading (gatk 220.127.116.11)
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.