I noticed if I have CNV calls that overlap like this

chr1:25000-50000 DEL
chr1:40000-100000 DEL

These two calls overlap but not by enough to be merged into one call. In the report file SV toolkit provides the output looks like this

chr1:25000-50000 DEL pval=0.2
chr1:40000-100000 DEL pval=NA

And this occurs for any overlapping calls.

Any suggestions to avoid this issue in SV toolkit?