GISTIC-segmentation overlaps error

Question

[LionisOne]

Dear All, I have few tumor data to screen out the true copy number variation analysis. I used CNVKIT for CN analysis with default parameters and I further, used cnvkit-gainloss function with Log2 threshold 0.6 for further filter out the low-level CN segments. But when I use this segment file for GISTIC run, it showing an error "several overlaps segments found". How can I fix this problem? Your great help is highly appreciated. Thanks in advance.

Answer 1

[Samarth Kulshrestha]

Hi,

Can you paste the input data (few lines) which you are using as INPUT for GISTIC program? I would like to check the data structure to understand the problem.

Thanks

[LionisOne]

@Samarth Kulshrestha,

Thanks. I figured it out!

[Pierre Lindenbaum]

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