Inference of structural variants from short read data is always sneaky (for a question about pair-end reads, see this). Recently I bumped into a paper where they used mate-pairs for inference of structural variants and it made me wonder if the approach might be problematic or not.
Mate-pairs have a known problem of contamination by pair-end reads and there is even a tool for calling structural variations considering this problem called SVachara. However, authors have used methods Lumpy and Delly2. Have they chosen an appropriate approach?
