How to import the output of CNVkit into GISTIC2.0 ?

Question

[Tonny]

Hi,

I get the many CNV results from sing cell genome sequencing with CNVkit. I'd like to get the driver CNV with GISTIC2.0. I have read the post Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.. There are two files, markerFile and segmentFile. Is there any way to obtain the files from the output of CNVkit?

Thanks.

Answer 1

[Eric T.]

It's not implemented as an "export" command in CNVkit yet, but here's the issue tracking that request: https://github.com/etal/cnvkit/issues/152

The segmentFile is just SEG format, so you can do cnvkit.py export seg *.cns -o gistic.segments to generate it.

For the markerFile, see Luca's notes in the linked issue. I think you can use the first 3-4 columns from cnvkit.py export jtv to get most of the way there.

[Tonny]

Thanks for your answer. I will try it.

[Tonny]

Hi Eric, I have tried the command as you mentioned. However, I failed to obtain the right markerFile. And I also tried to modify the start of segment with start_pos + 1. There were still segments with start or end positions do not match any markers in the markerFile. Finally, I found that 'As of GISTIC release 2.0.23, the markers file is an optional input - if omitted, pseudo markers are generated as uniformly as possible using the maxspace input parameter.'. So I use the segment file only to run GISTIC successfully.

[Eric T.]

Great, thanks for letting me & everyone know that the SEG export by itself will work.

[mike.rightmire]

I realize this is an older post, but I'm having some difficulties running GISTIC against the segments file created by cnvkit.py.

GISTIC_2_0_23.tar.gz MCR_R2014a_glnxa64_installer.zip CNVKIT

• Metadata-Version: 2.1
• Name: CNVkit
• Version: 0.9.9.dev0

I create the seg file using ...

cnvkit.py export seg tumor021-01.cns -o ${outdir}/.tumor021-01.seg

The file comes out looking like ...

chrom   chr_start       chr_stop        num_positions   normal_depth    tumor_depth     log2_ratio      gc_content
1       12946   13045   100     27.8    35.7    0.358   61.0
1       13046   13145   100     38.8    41.1    0.082   61.0

Do I need to manualy edit this file so that it's in accordance with the SEG file format mentioned in the GISTIC documentation, or can CNVKIT output it directly?