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.
Error handling end exit codes in GATK
I have a question regarding the error handling of GATK. Is GATK always returning a 0 exit status?
For example one of my bam files seems to be malformated, so the Haplotypecaller reports an error and stops.
So I was expecting my whole script to stop as I always check the return status $? in shell.
But it reports as "0", meaning my scripts goes on. Is there a way to catch these errors?
EDIT: I just noticed my pipeline was configured to use an old version of GATK.
With 3.6-0 it seems to be working. Sorry for the confusion.