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 is the power calculated?
When I run the following:
java -Xmx2g -jar muTect-1.0.27783.jar --analysis_type MuTect
I see a list of parameters, not fully documented. I noticed that the results are very sensitive to some of them. Precisely, I am most interested in the last three, which deal with the power calculation:
--power_constant_qscore --power_constant_af --absolute_copy_number_data
Could you please explain how the constants are used to calculate the power? Is the "absolute copy number data" necessary? Thank you.