Error when running GISTIC 2.0

[Hareem Ali]

Hi, 

I am working on cancer data and wish to use GISTIC to identify significant variations across the genome. I ran gistic with a combined seg file of 91 samples and used the hg38 refgene. I did not add a markers file. I got an error saying I have 14768 invalid chromosomes and the first invalid chromosome is '1990' on line 2. After running all I generated was a mat file called gistic_input.mat.

I was wondering if anyone could help me understand this error and how to fix it.

Thanks, 

Hareem

[Edwin Juarez]

Hello, 

I would suggest posting in the GISTIC forum about this particular question, as that is frequented by the method authors as well as frequent users of GISTIC.

Kind regards,

Edwin.