Does samtools depth know how to handle paired-end reads

Question

[roy.granit]

I wish to test the depth of coverage using samtools depth.. yet I'm not sure if it can handle well paired-end reads.. (assuming that if a BP is read twice due to PE this should not be counted into the coverage)

Does anyone have a clue? or suggestion for another (fast) tool calculates the coverage?

[ATpoint]

Just did a quick test with a file containing overlapping paired-end reads, and yes, samtools depth counts each mate separately, so a nucleotide spanned by one pair gets a depth of 2. There is an alternative implementation, sambamba depth, that offers the --fix-mate-overlaps option to avoid double-counting.