Hello,

This is the first time I use CNVkit, but I cannot understand output files well. So, I have some questions, please let me know.

There is no normal file and the cases are targeted sequencing. I ran CNVkit, and got 3 kinds of files (.cnn, .cnr, .cns). I understood .cnn.

1. I don't know why log2 is different between .cnn and .cnr.

It's a .cnn file.

chromosome  start   end gene    depth   log2

chr1    2488093 2488182 TNFRSF14    814.135 9.66912

chr1    2489154 2489283 TNFRSF14    768.636 9.58616

chr1    2489771 2489917 TNFRSF14    905.774 9.82301

It's a .cnr file.

chromosome  start   end gene    depth   log2    weight

chr1    2488093 2488182 TNFRSF14    814.135 -0.0856249  0.843844

chr1    2489154 2489283 TNFRSF14    768.636 -0.39928    0.870295

chr1    2489771 2489917 TNFRSF14    905.774 -0.268636   0.87808

1. I cannot find what "p_ttest" is.

There are no explains like its meaning, how to calculate it, or cut-off.

Thank you.