table of contents
| CNVKIT_EXPORT(1) | User Commands | CNVKIT_EXPORT(1) |
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
| January 2021 | cnvkit export 0.9.8 |