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.
How to get the min, max and average coverage for whole intervals (pre-defined in a bed file)?
I am working with DNA sequencing data (illumina). We use targeted sequencing mostly. I analysed the data following your best practice using GATK 184.108.40.206.
My question is: How can I simply generate a report where I can see, for each selected interval in a bed file, the minimum, maximum and average coverage. The available tools under "Coverage Analysis" and "Diagnostics and Quality Control" don't seem to provide such information. I think those tools were available under GATK3.8 but I can't see which ones in GATK4 are replacing them.
Thanks in advance