I have three mutation data sets from three different size gene panels, I want to combine the three data sets, divide the samples into two groups, and compare gene mutation rates between two groups.

first, I have tried to get overlapped bed-files region, but I only have two bed-files of these three gene panels, these three gene panels have different size, how can I combine them or how can I compare gene mutation rates between two groups using these three data sets?

Thanks!