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.
What is happening regarding Picard tools and NovaSeq?
I got picard 2.9.4 in order to get the support for CBCL files, i.e. NovaSeq output. There was a command line option 'USE_NEW_CONVERTER' added to IlluminaBasecallsToSam. Now in 2.10.0 that command-line option is gone. Also, I see some hints in the code that the functionality of ExtractIlluminaBarcodes has been folded into IlluminaBasecallsToSam. I couldn't find anything about these changes in the online documentation or the forum. Is there any documentation about these changes?