GISTIC 2.0 for sequencing data

Question

[vctrm67]

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?

[zizigolu]

Gistic2 works without marker file

I have a script calculating the marker file if you want

[vctrm67]

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

[zizigolu]

No it is not required

I have tried that

[vctrm67]

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

[zizigolu]

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

[vctrm67]

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

[zizigolu]

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

Creating marker file for GICTIC2