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.
Increase read depth for MuTect?
I am wondering how I could increase the amount of reads MuTect considers in its analysis. As an example, for the same sample VarScan2's output displays DP=20862 whereas MuTect's output VCF displays DP=989. This makes it harder to compare their respective outputs.
I look forward to some answers. I have looked around quite a bit and haven't found anything concerning this.