Why does GISTIC require a markers file?

Question

[Irsan]

In order to run GISTIC(2.0), you need at least:

1. Segmented copy numbers (.seg file, e.g. CBS output)
2. Gene annotation file in GISTIC format (refgene file)
3. A markers file that gives the genomic position of probes/windows that was used (before segmentation)

I wonder what GISTIC does with the markers file does and why it is required. To me it seems that all relevant information is already contained within the seg file?

[rse]

I have the same question? Do you know how to run GISTIC from BIC-seq cnv output?

Answer 1

[agicict]

Hi.

According to the original paper, the authors used GLAD to decrease noise.

If you open score.gistic file, you will notice that some of start and end column's numeric values don't present in segfiles but they are in marker files.

GISTIC scores each genomic marker with G scores.

Because of this, GISTIC requires marker file.

[agicict]

In my opinion, GISTIC seems to assign normalized log2ratio to genomic markers then calculate G score of each marker.