.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CNVKIT_IMPORT-SEG "1" "January 2021" "cnvkit import-seg 0.9.8" "User Commands"
.SH NAME
cnvkit_import-seg \- Convert a SEG file to CNVkit .cns files.
.SH DESCRIPTION
usage: cnvkit import\-seg [\-h] [\-c CHROMOSOMES] [\-p PREFIX] [\-\-from\-log10]
.TP
[\-d DIRECTORY]
segfile
.SS "positional arguments:"
.TP
segfile
Input file in SEG format. May contain multiple
samples.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-c\fR CHROMOSOMES, \fB\-\-chromosomes\fR CHROMOSOMES
Mapping of chromosome indexes to names. Syntax:
"from1:to1,from2:to2". Or use "human" for the preset:
"23:X,24:Y,25:M".
.TP
\fB\-p\fR PREFIX, \fB\-\-prefix\fR PREFIX
Prefix to add to chromosome names (e.g 'chr' to rename
\&'8' in the SEG file to 'chr8' in the output).
.TP
\fB\-\-from\-log10\fR
Convert base\-10 logarithm values in the input to
base\-2 logs.
.TP
\fB\-d\fR DIRECTORY, \fB\-\-output\-dir\fR DIRECTORY
Output directory name.