This software can merge and intersect with the logic of SUrVIVOR, considering the breakpoints.
mamba create -n surpyvor python==3.7
mamba install -c bioconda surpyvor
# Intersect SV vcf
surpyvor highconf --variants 15X_long.vcf 15X_NGS.vcf -d 10 -o isec.vcf
# Union
surpyvor highsens --variants 15X_long.vcf 15X_NGS.vcf -d 10 -o union.vcf
# Venn
surpyvor venn --variants 15X_long.vcf 15X_NGS.vcf -d 10 --plotout PLOTOUT --keepmerged -i