Compatibility and other I/O


Convert Picard CalculateHsMetrics coverage files (.csv) to the CNVkit .cnn format.


Convert a file in the SEG format (e.g. the output of standard CBS or the GenePattern server) into one or more CNVkit .cns files.

The chromosomes in a SEG file may have been converted from chromosome names to integer IDs. Options in import-seg can help recover the original names.

  • To add a “chr” prefix, use “-p chr”.
  • To convert chromosome indices 23, 24 and 25 to the names “X”, “Y” and “M” (a common convention), use “-c human”.
  • To use an arbitrary mapping of indices to chromosome names, use a comma-separated “key:value” string. For example, the human convention would be: “-c 23:X,24:Y,25:M”.


Convert copy number ratio tables (.cnr files) to another format.

A collection of probe-level copy ratio files (*.cnr) can be exported to Java TreeView via the standard CDT format or a plain text table: export jtv *.cnr -o Samples-JTV.txt export cdt *.cnr -o Samples.cdt

Similarly, the segmentation files for multiple samples (*.cns) can be exported to the standard SEG format to be loaded in the Integrative Genomic Viewer (IGV): export seg *.cns -o Samples.seg

Also note that the individual .cnr and .cnn files can be loaded directly by the commercial program Biodiscovery Nexus Copy Number, specifying the “basic” input format.