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.
I run into the errors below, when I try to run the StructuralVariationDiscoveryPipelineSpark to discover structural variants in a given sample:
ERROR Executor: Exception in task 0.0 in stage 5.0 (TID 50)
java.lang.IllegalArgumentException: provided start is negative: -36
I am not sure why the tool has to throw up these errors when every other thing seems fine. I wiil appreciate if you could shed some light on this.