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