Paired reads that overlap introduce additional complexity for variant detection. This section describes how this is handled by CLC Genomics Workbench.
When it comes to coverage in the overlapping region, each pair is contributing once to the coverage. Even if there are indeed two reads in this region, they do not both contribute to coverage. The reason is that the two reads represent the same fragment, so they are essentially treated as one.
When it comes to counting the number of forward and reverse reads, including the forward/reverse reads balance, each read contribute. This is because this information is intended to account for systematic sequencing errors in one direction, and the fact that the two reads are from the same fragment is less important than the fact that they are sequenced on different strands.
If the two overlapping reads do not agree about the variant base, they are both ignored. Please note that there can be a special situation with the basic variant detection: If the two reads disagree, and one read does not pass the quality filter, the other read will contribute to the variant just as if there had been only that read and no overlapping pair.