Consolidate peak lists?

[asiangg]

I'm trying to combine information from the peak lists of more than two (usually three) biological replicates. However, I encountered some difficulties.

How to combine the three peak lists considering one peak from a biological replicate can overlap with several peaks from another replicate? Does anyone have any good method or has developed any tool for this?

To be more specific about what I'm trying to do, the information for each peak contains chr, start, end and normalized IP read count.

Thanks!

[mgogol]

Galaxy has some useful tools for interval combination under "Operate on genomic intervals".

I'm not sure if it's quite what you're after.