.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_FIX "1" "March 2019" "cnvkit_fix 0.9.5" "User Commands"
.SH 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.
    
.SH DESCRIPTION
usage: cnvkit fix [\-h] [\-\-no\-gc] [\-\-no\-edge] [\-\-no\-rmask] [\-i SAMPLE_ID]
.IP
[\-o FILENAME]
target antitarget reference
.SS "positional arguments:"
.TP
target
Target coverage file (.targetcoverage.cnn).
.TP
antitarget
Antitarget coverage file (.antitargetcoverage.cnn).
.TP
reference
Reference coverage (.cnn).
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-no\-gc\fR
Skip GC correction.
.TP
\fB\-\-no\-edge\fR
Skip edge\-effect correction.
.TP
\fB\-\-no\-rmask\fR
Skip RepeatMasker correction.
.TP
\fB\-i\fR SAMPLE_ID, \fB\-\-sample\-id\fR SAMPLE_ID
Sample ID for target/antitarget files. Otherwise
inferred from file names.
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output file name.