Question: GISTIC 2.0 for sequencing data
0
gravatar for vctrm67
7 weeks ago by
vctrm6720
vctrm6720 wrote:

I am looking to hopefully run GISTIC 2.0 on some CNV calls I have from sequencing data. However, the input file requires the following fields:

(1) Sample      (sample name)
(2) Chromosome      (chromosome number)
(3) Start Position      (segment start position, in bases)
(4) End Position      (segment end position, in bases)
(5) Num Markers      (number of markers in segment)
(6) Seg.CN      (log2() -1 of copy number)

I am not sure how to fill in the "Num Markers" field, given that I only have sequencing data. I read in this link that it should be the number of heterozygous SNPs in each segment. Is there a way to get this information?

sequencing cnv cna wgs gistic • 166 views
ADD COMMENTlink written 7 weeks ago by vctrm6720

Gistic2 works without marker file

I have a script calculating the marker file if you want

ADD REPLYlink written 7 weeks ago by A3.9k

I am referring to the segmentation file in the documentation. The Num Markers field seems to be required by the segmentation file.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by vctrm6720

No it is not required

I have tried that

ADD REPLYlink written 7 weeks ago by A3.9k

But then how would I format the segmentation file to not include it? What would I put for Num Markers in the column?

ADD REPLYlink written 7 weeks ago by vctrm6720

I told you I have a script to do that You called copy number with which software?

ADD REPLYlink written 6 weeks ago by A3.9k

I do not know which software. Is that necessary? What does your script put for Num Markers instead?

ADD REPLYlink written 6 weeks ago by vctrm6720

By the way I had already asked this question here and got answer

Creating marker file for GICTIC2

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by A3.9k
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