CNVKIT_FIX

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).

options:

-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.