Command: normalize

Calculate normalized rates of events in a .ccf file

Required parameters:

  • -i, –input INPUT: input .ccf file

  • -o, –output OUTPUT: Output file (bedGraph format)

Optional parameters:

  • -r, –regions REGIONS: Regions over which to normalize event counts; should be supplied as a BED file. If not provided, the input file will be segmented using Bayesian blocks. (all options from blockify segment are available)

  • -k, –libraryFactor LIBRARYFACTOR: Normalization factor for library size (default: 1000000)

  • -l, –lengthFactor LENGTHFACTOR: Normalization factor for the length of regions; used to calculate scaled rates of events per interval (default: None)