Does anyone know if BWA Mem -M flag (mark shorter split hits as secondary) will have a detrimental effect on structural variation calling using split reads with Delly? 

I orignially added it to my BWA mapping pipeline for compatibility with Picard/GATK but I believe that issue has been resolved in GATK4.  Now wondering if it's even necessary and if it will have an effect on SV calls that use split reads. 

Input to this pipeline may include paired, single end, interleaved or split data from illumina, ion torrent, or nanopore. 
For [delly][1], it doesn't make a difference if split reads are marked as secondary or supplementary.

  [1]: https://github.com/dellytools/delly