Question: GISTIC input parameters.
gravatar for rin
11 months ago by
rin30 wrote:

Hi everyone

I am running GISTIC 2.0 in segmentation data from TCGA and I was wondering whether it is advisable to set the input parameters as default or change the different thresholds. Running the analysis with everything on default and by only changing the confidence level to 0.99, I got many regions amplified/deleted so I thought of making the significance criteria more strigent. What would be your advice? Is this kind of plot considered "normal" output?

Here is how a plot I get looks like for example. enter image description here

Thank you in advance!

UPDATE: Followed some recommendations on the GISTIC forum, but still I get many amplified and deleted regions. Any help on how I could extract any meaningful results from such noisy plots?

cnv snp gistic • 1.2k views
ADD COMMENTlink modified 4 weeks ago by achernia10 • written 11 months ago by rin30
gravatar for Amitm
11 months ago by
Amitm1.6k wrote:

Hi, Did you provide the 'control' CNV data using the -cnv param? That param can be used provide segments that are seen in healthy pop. and/ or control samples. The GISTIC repo. has a file provided for that param, under here -

Pick the file CNV.hg19.bypos.111213.txt See if that helps.

Also, I am not sure if you have access to segments seen in the controls samples for the TCGA cancer type you are looking at. If you have, then it is probably a good idea to subtract such segments from the tum. sample segments first.

Segments that have reverse overlap satisfying >=50% are good candidates to filter out. Try

ADD COMMENTlink written 11 months ago by Amitm1.6k

Thanks for your answer! I was not aware for that option, but I cannot use it as my data are mapped on hg38. TCGA masked copy number data might be an alternative I guess? (They include only somatic variations while germline variations are filtered out)

ADD REPLYlink written 11 months ago by rin30

Indeed, you can just start from the pre-processed GISTIC 2.0 data, hosted on Broad Firebrowse. This will contain somatic copy number alterations (sCNA).

ADD REPLYlink modified 9 months ago • written 9 months ago by Kevin Blighe46k
gravatar for achernia
4 weeks ago by
achernia10 wrote:


It looks like the file you are using has not been filtered for germline CNVs. If anyone of you out there have questions about GISTIC, write to us directly at the Broad instead of posting on Biostars!

ADD COMMENTlink written 4 weeks ago by achernia10
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