Visualizing aCGH in IGV and deletions overlapping amplifications?

Question

[Avro]

Hi everyone,

I have analyzed my aCGH data with JISTIC (improvement over the Broad Institute’s GISTIC). Then, I used the Broad’s IGV to visualize it. Several people told me to do so to look for regions that show up both as deletions and amplifications. My question is: do you know how could this be? Is it be because of the heterogenous nature of the sample? I would greatly appreciate your input.

Thank you!

[Chirag Nepal]

Could you please share how did you prepare your data to run JISTIC.

Thanks !