Question: How to import the output of CNVkit into GISTIC2.0 ?
gravatar for Tonny
9 weeks ago by
Shanghai, China
Tonny20 wrote:


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?


gistic2.0 cnvkit • 220 views
ADD COMMENTlink modified 9 weeks ago by Eric T.1.9k • written 9 weeks ago by Tonny20
gravatar for Eric T.
9 weeks ago by
Eric T.1.9k
San Francisco, CA
Eric T.1.9k wrote:

It's not implemented as an "export" command in CNVkit yet, but here's the issue tracking that request:

The segmentFile is just SEG format, so you can do 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 export jtv to get most of the way there.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Eric T.1.9k

Thanks for your answer. I will try it.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Tonny20

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.

ADD REPLYlink written 7 weeks ago by Tonny20

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

ADD REPLYlink written 7 weeks ago by Eric T.1.9k
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