If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Germline CNV, the correct order of using the involved tools.
I know that the tutorial is not available yet for the Germline CNV and it is still in beta, but can anyone just write some numbered points about the order of the involved tools please? just as points. To my understanding it is something like this:
4- post processing to get the vcf file
Are those steps enough to be considered? Or are there any extra beneficial steps that might be added in between?
Many thanks for the help