Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

java.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam without read groups

hgiblinghgibling Member
edited March 2016 in Ask the GATK team


When running Picard's SamToFastq with 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.

Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


Sign In or Register to comment.