Compatibility and other I/O¶
import-picard¶
Convert Picard CalculateHsMetrics coverage files (.csv) to the CNVkit .cnn format.
import-seg¶
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”.
export¶
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:
cnvkit.py export jtv *.cnr -o Samples-JTV.txt
cnvkit.py 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):
cnvkit.py 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.