.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CNVKIT-REFERENCE2TARGETS "1" "January 2021" "cnvkit-reference2targets 0.9.8" "User Commands"
.SH NAME
cnvkit-reference2targets \- Extract target and antitarget BED files from a CNVkit reference file.
.SH DESCRIPTION
usage: cnvkit\-reference2targets [\-h] [\-o OUTPUT] reference
.PP
Extract target and antitarget BED files from a CNVkit reference file. Once you
have a stable CNVkit reference for your platform, you can use this script to
drop the "bad" bins from your target and antitarget BED files and avoid
unnecessarily calculating coverage in those bins during future runs. This
script is also useful to recover the target and antitarget BED files that
match the reference if those BED files are missing or you're not sure which
ones are correct.
.SS "positional arguments:"
.TP
reference
Reference file.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
Output base name (extensions added automatically).