Man page - cnvkit-export(1)

Packages contains this manual

Package:  cnvkit
apt-get install cnvkit

Manuals in package:
• cnvkit-import-theta(1)
• cnvkit-coverage(1)
• cnvkit-metrics(1)
• cnvkit-import-seg(1)
• cnvkit-export(1)
• cnvkit-breaks(1)
• cnvkit-fix(1)
• cnvkit-segmetrics(1)
• cnvkit-batch(1)
• cnvkit-import-rna(1)
• cnvkit-bintest(1)
• cnvkit-diagram(1)
• cnvkit-call(1)
• cnvkit-autobin(1)
• cnvkit-access(1)
• cnvkit-antitarget(1)
• cnvkit-sex(1)
• cnvkit-segment(1)
• cnvkit-genemetrics(1)
• cnvkit-heatmap(1)
• cnvkit-target(1)
• cnvkit-import-picard(1)
• cnvkit-reference(1)
• cnvkit-scatter(1)
Documentations in package:
• cnvkit

Manual

CNVKIT_EXPORT

NAME
DESCRIPTION
positional arguments:
options:

---

NAME

cnvkit_export - Convert CNVkit output files to another format.

DESCRIPTION

usage: cnvkit.py export [-h]
{bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic}

...

positional arguments:

{bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic}

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.

gistic

options:

-h , --help

show this help message and exit

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