Matrix plot of deleted positions vs reference genome

Question

[samuel.lipworth]

Hi,

I want to plot positions which don't align to my reference genome at their respective position - eg. 1,5,7,11 for genome 1, 1,4,5,7,10,11 for genome 2. I would like the positions which don't align to be represent by bars or any other symbol so that I can compare deletions across multiple samples vs the reference genome graphically. Anybody have any ideas how to do this?