Please take a look at the example here: GCmodel adjustment. The GCModel file should come with the package when you download it.
If the GCModel file does not exist, then take a look at the FAQ in order to see how you could produce one:
- How to use genomic wave adjustment independent of CNV calling?
Some users just want to adjust signal intensity values, without generating CNV calls by PennCNV. The genomic_wave.pl program in PennCNV package can be used to adjust signal intensity values. The input file must have a field in the header line that says "*.Log R Ratio". The -adjust argument can be used to generate a new file with updated Log R Ratio measures. This procedure can be also used in Agilent arrays or Nimblegen arrays for adjustment. Use the cal_gc_snp.pl script to generate GC model file for these custom arrays.