.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_EXPORT "1" "March 2019" "cnvkit_export 0.9.5" "User Commands"
.SH NAME
cnvkit_export \- Convert CNVkit output files to another format.
.SH DESCRIPTION
usage: cnvkit export [\-h]
.IP
{bed,seg,vcf,theta,nexus\-basic,nexus\-ogt,cdt,jtv} ...
.SS "positional arguments:"
.TP
{bed,seg,vcf,theta,nexus\-basic,nexus\-ogt,cdt,jtv}
Export formats (use with \fB\-h\fR for more info).
.TP
bed
Convert segments to BED format. Input is a
segmentation file (.cns) where, preferably, log2
ratios have already been adjusted to integer absolute
values using the 'call' command.
.TP
seg
Convert segments to SEG format. Compatible with IGV
and GenePattern.
.TP
vcf
Convert segments to VCF format. Input is a
segmentation file (.cns) where, preferably, log2
ratios have already been adjusted to integer absolute
values using the 'call' command.
.TP
theta
Convert segments to THetA2 input file format
(*.input).
.TP
nexus\-basic
Convert bin\-level log2 ratios to Nexus Copy Number
"basic" format.
.TP
nexus\-ogt
Convert log2 ratios and b\-allele freqs to Nexus
"Custom\-OGT" format.
.TP
cdt
Convert log2 ratios to CDT format. Compatible with
Java TreeView.
.TP
jtv
Convert log2 ratios to Java TreeView's native format.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit