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.
Using CRAM files in Picard SamToFastq with Queue
I'm trying to convert CRAM files to FASTQ format with SamToFastq as part of a pipeline I have written in a Queue script. Is there any parameter for passing a reference file in the SamToFastq Queue module? I didn't see any such parameter in SamToFastq.scala, PicardBamFunction.scala, or JavaCommandLineFunction.scala. I couldn't find anything on the forum, and I tried a bunch of different things by guessing, but didn't have any luck. If there is no parameter to use a reference file in a Queue script for Picard tools, is there any sort of workaround (e.g., environment variable that Picard will pick up on)?