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.
java.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam without read groups
When running Picard's
OUTPUT_PER_RG=T on a bam file without read group information, you get the following error:
Exception in thread "main" java.lang.NullPointerException at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:148) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:119)
Obviously the command shouldn't work if there is no read group information, but it would be nice if there was a more informative error provided, as the
NullPointerException makes it seem like an issue with memory allocation.