I am testing the PennCNV software using input data from Illumina final report data, and I was able to generate a .PFB file for my samples. However I missed something in the PennCNV official guide beacuse I couldn't find how to build or obtain the .HMM model file used for cnv call detection. I guess I should build the file from my own dataset but it seems there is no guidance about it.
From the documentation:
The HMM file supplied the HMM model to PennCNV, and tells the program what would be the expected signal intensity values for different copy number state, and what is the expected transition probability for different copy number states
How do you get the transition probabilities, mean signal intensity values and standard deviation, in order to build the .hmm file?