how coverage in region is calculated

[Xiaoyun Guo]

Hi

Thanks for developing this great tool!

I have a naive question, how is the coverage in a region calculated? Is it reads per unit length? so if I normalized the coverage with library size and x1e9, I got RPKM?

Thanks

[Brent Pedersen]

The coverage is the number of aligned bases (meeting mapq threshold) that cover each region base.
Note that when using --fast-mode deletions will also be counted as aligned bases.