cnvkit-export(1)
Convert CNVkit output files to another format.
Description
CNVKIT_EXPORT
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. |
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|
jtv |
Convert log2 ratios to Java TreeView’s native format. |
options:
-h, --help
show this help message and exit