GISTIC2.0 Create Marker File from CNVkit output

[James Moon]

Hello. I am trying to create a markers file based on CNVkit output [.seg, .cnr, .cns, targetcoverage.cnn file] for GISTIC2.0.

I have a reference genome file and segmentation file ready, but I need more information about on the markers file.

From the user guide, it describes as:

The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three-column, tab-delimited file with an optional header. The column headers are: 1. Marker Name (marker name) 2. Chromosome (chromosome number) 3. Marker Position (in bases).

I am not sure where I can get the maker name from the CNVkit output.

Thanks!

James

[Edwin Juarez]

Hello James,

For questions that relate to GISTIC analyses and results interpretation, please contact the GISTIC forum at https://groups.google.com/a/broadinstitute.org/forum/#!forum/gistic-forum (note that you may need to click "join group" in order to access their forum).

Edwin.