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.