How to get a comperative result of 2 bed files?

Question

[herh]

I had a bed file, output of a CNV prediction software containing the columns name, chromosome, starting_index, ending_index and prediction(duplicate or deletion). I need to give a numerical result for this output. I have the bam, bam.bai and bed files of the original dataset. How can give a measurement of the output and which tools I can use?

[Pierre Lindenbaum]

what kind of measurement do you need ? I see one bed file in your description , what are the TWO bed file ?

[herh]

Actually, I am asked to use truvari tool but it works with vcf datasets. So, indeed I need a benchmarking measurement. One bed file is the output of the program which gives a prediction of deletion or duplication. The other bed file contains 5 columns; chromosome, ID, one column has a number range between 0 and 1.

[Pierre Lindenbaum]

convert the bed to vcf and use truvari.