NAME

       cnvkit_fix - Combine target and antitarget coverages and correct for biases.

           Adjust raw coverage data according to the given reference, correct potential
           biases and re-center.

DESCRIPTION

       usage: cnvkit fix [-h] [-c] [-i SAMPLE_ID] [--no-gc] [--no-edge] [--no-rmask]

              [-o FILENAME] target antitarget reference

   positional arguments:
       target Target coverage file (.targetcoverage.cnn).

       antitarget
              Antitarget coverage file (.antitargetcoverage.cnn).

       reference
              Reference coverage (.cnn).

   optional arguments:
       -h, --help
              show this help message and exit

       -c, --cluster
              Compare and use cluster-specific values present in the reference profile. (Requires
              that the reference profile was built with the --cluster option.)

       -i SAMPLE_ID, --sample-id SAMPLE_ID
              Sample ID for target/antitarget files. Otherwise inferred from file names.

       --no-gc
              Skip GC correction.

       --no-edge
              Skip edge-effect correction.

       --no-rmask
              Skip RepeatMasker correction.

       -o FILENAME, --output FILENAME
              Output file name.