Are there any well developed tools that convert SV breakpoints in bedpe or any other formats to VCF and properly generate BND / DEL / DUP format SVs?
Options I have explored:
svtools bedpetovcf: requires a very involved specific bedpe input, and generating this input would be more work than writing my own conversion to vcf
breakpointGRangesToVCF: seems to have been removed from the StructuralVariantAnnotation package unfortunately