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.

HaplotypeCallerSpark stack overflow

Dear colleagues
All my attempts to use GATK HaplotypeCallerSpark with the option --spark-master local[*] fail because of stack overflow error with a similar error message as in
My GATK version is, that was installed via bioconda. On the github page describing the problem I have it is indiocated that this problem should be solved on Q2. Should I wait for the corrected version or is there a way to circumvent the problem with extra install or by using options like --java-options '-XssOptimalValue'?
When is the corrected version expected? Is Q2 (end of June?) still an option? Will it be readily on bioconda then?


Sign In or Register to comment.