Are duplicates counted by samtools depth and mpileup?

[abalter]

I'm seeing a number of forum posts claiming that samtools depth ignores duplicates. However, there is nothing about this in the documentation.

1. Are duplicates counted?
2. Does it matter if the bam file has the duplicates marked (e.g. by Picard markdups).

References

https://www.biostars.org/p/195497/

https://www.biostars.org/p/60841/

[dpryan79]

1. If they aren't marked as duplicates then they're included.
2. If they're marked (in the flag by any program) then they're excluded.

Regarding samtools mpileup, note the --ff options, which controls this.