I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome.
For example, I've created a bed file with 1 chromosome. When I input my BAM file and the BED file, I get the following output:
chr1 0 249250621 103718897 224950839 249250621 0.9025086
I know the first 3 fields are from my chr BED file, the 4th field is the # of reads, 5th is # of bases covered, 6th is length of chromosome (redundant to field 3), and the last column is the fraction of bases covered (5th field/6th field).
So the 7th/last field gives the breadth of coverage, but I don't see a depth of coverage value. How do I get a depth of coverage?