Yes, that's what I thought that you meant. It's not a traditional metric that 's observed but I have to admit that it's interesting and I think that I'll calculate it in my analyses in the future. Thanks!

Anyway, I have been able to do this just now indirectly using BEDTools and looking over the hg38 reference genome:

Bases at 0 read depth:

bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1

Bases at >0 read depth:

bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1

The genomecov function of BEDTools normally computes coverage in your BAM file for each position in your supplied reference genome. The output looks like this:

chr1    0   11794364    0
chr1    11794364    11794488    3
chr1    11794488    11794490    5
chr1    11794490    11794514    6
chr1    11794514    11794639    3
chr1    11794639    14022492    0
chr1    14022492    14022535    1
chr1    14022535    97082336    0
chr1    97082336    97082442    1
chr1    97082442    97082486    2
chr1    97082486    97082593    1
chr1    97082593    97305303    0
chr1    97305303    97305377    2

I then use the awk commands to calculate total bases at 0 read depth and total bases >0 read depth. After that, the calculation for percentage can easily be done. For my sample (a small targeted sequence panel), I ended up with:

34312 non-zero bases
3209251793 zero bases
(34312 / (3209251793 + 34312 )) * 100 = 0.0011% genome coverage

It took less than a minute to run with my commands above.

If you want to automate this in a pipeline, the following code would work (note that in BASH decimal points need to be handled specially with the bc command):

zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1)

nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1)

percent=$(bc <<< "scale=6; ($nonzero / ($zero + $nonzero))*100")

echo $percent

Like I said, I think that this is a useful metric and you could perhaps turn this into a tutorial(?), if Pierre agreed too.