I have seen the question briefly discussed in specific contexts, but as it seems like there is no consensus between different tools on this issue I think it would be useful to report here what the best practice is.
So I have Illumina MiSeq paired-end reads. Let's say a region is covered by a single pair of reads (one forward/one reverse), should the coverage in the overlapping region reported as 1x or 2x? What are the arguments for each?
Here is an illustration here: https://bioinformatics.stackexchange.com/questions/5427/double-counting-coverage-of-overlapped-read-pairs/5473