cnvkit-fix1
Combine target and antitarget coverages and correct for biases. adjust raw coverage data according to the given reference, correct potential biases and re-center.
Overview
usage: cnvkit.py 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
--clusteroption.)
-
-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.
Releases
4 releases since Debian 10 (Buster); the text changed 3 times.
--cluster since Debian 11 (Bullseye);
-c since Debian 11 (Bullseye).