Use Sequenza output to run GISTIC2

Question

[qxiong1]

From Sequenza output, there are following 13 columns, I am wondering which one I should use for GISTIC2 to calculate Set.CN?

"chromosome" "start.pos" "end.pos" "Bf" "N.BAF" "sd.BAF" "depth.ratio" "N.ratio" "sd.ratio" "CNt" "A" "B" "LPP"

Answer 1

[Thind amarinder]

It is worth taking a look into this post

http://crazyhottommy.blogspot.com/2017/11/run-gistic2-with-sequenza-segmentation.html