Gistic2.0 Segment overlap error

[Matt Moravec]

Hi, I am using gistic2.0 to with the ref file set as hg38, and I uploaded my segmentation file, which I will attach here. When I first had the error there were duplicate patients. After removing all duplicates I still had the error, but with less overlaps detected. This si the error message.

GISTIC version 2.0.23
 
GISTIC 2.0 input error detected:
312 segment overlaps detected in file '/opt/gpcloud/gp_home/users/miRDriver/uploads/tmp/run1890416837164653985.tmp/seg.file/1/ovary_cnv_sample_formatted_6.txt'.
First overlap detected between segments at lines 5 and 535.

When I investigated lines 5 and 535, I saw that they were different and therefore I do not understand what is causing the error.

My job number is 

245687. GISTIC_2.0

[GenePattern Help Forum]

Hello, 

I think you will find this thread in the GISTIC-Forum helpful: https://groups.google.com/a/broadinstitute.org/g/gistic-forum/c/unYY5vDfdMc/m/SUEmSPapCAAJ

Specifically - segments should not overlap by more than 1 marker. 

The stop position of line 5 overlaps greatly with the start position of line 535. This is particularly apparent if you view your file sorted by the first column.

I hope this helps,

Barbara

[Matt Moravec]

Thanks!

[Hanie Azari]

Dear Matt,

I also face this issue, did you find any solution?

thanks,

Hanieh A