I have a reference genome and now I would like to call structural variants from Illumina pair-end whole genome resequencing data (insert size 700bp).
There are many tools for SV calls (I made an incomplete list of tools bellow). There is also a tool for merging SV calls from multiple methods / samples - SURVIVOR. Is there a combination of methods for SV detection with optimal balance between sensitivity and specificity?
There is a benchmarking paper, evaluating sensitivity and specificity of SV calls of individual methods using simulated pair-end reads. However, there is no elaboration on the combination of methods.
List of tools for calling structural variants: