In the documentation for samtools (http://www.htslib.org/doc/samtools.html) the depth command has the following options:
-a : Output all positions (including those with zero depth)
-a -a, -aa : Output absolutely all positions, including unused reference sequences. Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.
I was wondering why there needs to be these two options and what unused reference sequences means? Why is the reference sequence sometimes unused vs. simply having no coverage there i.e. zero depth?