bwa-mem -M parameter and SV detection software compatability

[choijae3]

I wanted to ask people with experience using bwa mem to align their reads and use the bam file to detect SVs using programs such as pindel, breakdancer, CNVnator, svdetect.

I know that the -M parameter is pretty much needed for downstream picard compatibilty for marking duplicates however wouldn't the -M parameter eliminate reads that the SV detecting programs use?

Anyways I was wondering what people have experience when using bwa-mem for SV detecting.
Thanks