Determining Each Samples Coverage Area

First time I am working with NGS data. I've got a BAM file with mapped reads for my samples and a BED file with the regions in HG19 that were targeted (used an Ion-torrent ampliseq panel). Are there any tools that can output something similar to this:

**Sample      Amplicon           Chromosome           Start_coordinate_of_coverage             End_coordinate_of_coverage**
Sample1       amp_001                chr6                 1,000,000                                   1,000,250
Sample2       amp_001                chr6                 1,000,111                                   1,000,255
Sample1       amp_002                chr6                 1,000,200                                   1,000,333

I basically want to know for each gene what coverage we have for each sample.

EDIT: changed column headings, I'm looking for coordinates that have coverage, not depth at each exon.