Compatibility and other I/O

import-picard

Convert Picard CalculateHsMetrics per-target 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.

bed

The segmented output from multiple samples (*.cns) can be exported to BED format to support a variety of other uses, such as viewing in a genome browser. The log2 ratio value of each segment is converted and rounded to an integer value, as required by the BED format. To get accurate copy number values, see the call command.

# Estimate integer copy number of each segment
cnvkit.py call Sample.cns -y -o Sample.call.cns
# Show estimated integer copy number of all regions
cnvkit.py export bed Sample.call.cns --show-neutral -y -o Sample.bed

The same format can also specify CNV regions to the FreeBayes variant caller with FreeBayes’s --cnv-map option:

# Show only CNV regions
cnvkit.py export bed *.call.cns -o all-samples.cnv-map.bed

Copy-number-neutral regions are not shown in the output by default, but can be included with the --show-neutral option.

cdt, jtv

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

seg

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

nexus-basic

The format nexus-basic can be loaded directly by the commercial program Biodiscovery Nexus Copy Number, specifying the “basic” input format in that program.