QC pipeline: Double-counting variants in overlapping mates

[NickSto]

The current QC pipeline counts variants twice when they occur in the overlapping region between mates in a pair.

This is due to the Naive Variant Caller just counting raw numbers of variants. But if a variant occurs in a position where both reads in a pair observe it, both reads will contain it, despite it only being present in the original fragment once.

[NickSto]

One solution would be to replace the NVC with another variant caller, like Freebayes or Detect.