NAME

       cnvkit_export - Convert CNVkit output files to another format.

DESCRIPTION

       usage: cnvkit export [-h]

              {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv} ...

   positional arguments:
       {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv}
              Export formats (use with -h for more info).

       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.

       seg    Convert segments to SEG format. Compatible with IGV and GenePattern.

       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.

       theta  Convert segments to THetA2 input file format (*.input).

       nexus-basic
              Convert bin-level log2 ratios to Nexus Copy Number "basic" format.

       nexus-ogt
              Convert log2 ratios and b-allele freqs to Nexus "Custom-OGT" format.

       cdt    Convert log2 ratios to CDT format. Compatible with Java TreeView.

       jtv    Convert log2 ratios to Java TreeView's native format.

   optional arguments:
       -h, --help
              show this help message and exit