Hello,

I have recently come across the gviz package in R and I am amazed by the things one can do with it. I find the alignment track especially useful for visualizing alignments from bam files. 

My problem lies in the fact that I have a bam file and I want to highlight only the GC positions which do not match with the  reference. Is there a way to specifically highlight the GC mismatches instead of all nucleotides which do not match?

Thanks,

Shounak