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.
What to do if the read group information is not properly available?
There are recommendations how to work with read groups (https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups)
However, I was wondering how to proceed if the read group information is not properly available - so when I am working with public data. SRA strips/replaces the read names from the fastq files so I basically only have a run, experiment and biosample ID from SRA. I am aware that working with public data is always difficult but I am trying to find the best possible way to handle this.
Thanks for your input!