The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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?