It's there any GISTIC2.0 like tools?

Question

[MatthewP]

Hello, I re-edit this question, orginal question:
GISTIC2.0 can find CNV across a set of samples. I want to know it's there other tools can do the same thing? Thanks.

New question:
So GISTIC2.0 is more suitable for array CGH data, for example GISTIC2 requires markers file(-mk) which WES/WGS can't afford(We can build by-hand, but this making -mk useless, right?). It's there any tool implement GISTIC to WES/WGS data?

I use cnvkit to get cnv seg file by the way.

[German.M.Demidov]

but wait, GISTIC2.0 is not a CNV caller. It is a tool for driver genes discovery. Can you clarify what you need - cancer driver genes discovery or CNV calling? Why do you need another tool? Because you can not call variants with GISTIC2.0 or because you are not satisfied with the algorithm? I'd say GISTIC2.0 algorithm sounds bullet-proof for me.

[jared.andrews07]

GISTIC calls CNVs for you, it just doesn't do segmentation. Though yes, it also does driver gene discovery, so a clarification would be nice.

[German.M.Demidov]

I am confused. Copy-number estimation is required by GISTIC as input (ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm , segmentation file paragraph). Clearly it requires Seg.CN as input. In which sense it calls CNVs?

[jared.andrews07]

Segmentation is breaking up the genome and estimating CN for each segment. However, these segments may be noisy and aren't stitched together into contiguous regions of CN change by segmentation algorithms alone.

GISTIC (and most other CNV programs/packages) utilize segmentation to perform CNV "calling" and to come up with discrete regions of CN change based on threshold values (often removing low-quality segments e.g. those with very few reads/probes). Often, a comparison to normals will also be done to remove germline changes, particularly if small focal changes are of interest.

This distinction is admittedly somewhat semantic, but generally the "calling" step is where hard thresholds are drawn and integer CN values are assigned. GISTIC does this.

[German.M.Demidov]

Ah, I see. That's kinda weird - GISTIC has no idea about the underlying sub-clonal structure, so I'd never use it for calling, but good to know that it also does that, thanks!

[cpad0112]

you can try other algorithms: haar segmentation (CNVkit supports as I understand), CBS implemented in DNAcopy @ MatthewP

Answer 1

[jared.andrews07]

There are lots of them:

• CNVkit
• CNVnator
• copyCat

Are just a few off the top of my head. CNVkit is probably the easiest to use out of those and can work on arrays or WGS. There are many others you can find just by searching a bit.

[MatthewP]

Sorry, I misunderstand function of gistic. I thought it's use to identify CNV from multiple samples, like some kind of merge many CNV results.

[jared.andrews07]

It kind of does that. It basically finds the recurrent CNVs between samples and tries to tie them back to which genes are affected.