Or you can use tail to return everything but the first line (if your track line is the first line). If you want to add more fields to the bed file, you can insert them in the print statement (I don't remember the minimum requirement for ChIPpeakAnno).
It's not clear that a simple format conversion is what you want . . .
In your question, you ask about "collapsing" a bedGraph file. This isn't trivial, and this problem is exactly what peak-callers like MACS solve.
The bedGraph format is typically used to visualize the genome-wide "signal". If it's output from a MACS run, the bedGraph will not be just the peaks, rather, it will show the coverage of all your reads shifted by d/2. It will have many, many more lines than a BED-format "peaks file" (try running wc -l on your files to confirm).
If your goal is to get a Venn diagram to compare peaks of two treatments, then comparing a BED file with a converted bedGraph file will not result in a meaningful diagram. Instead, you'll need to re-run a peak caller to get a BED file of peaks for each treatment.