vcf2diploid personal genome constructor, it can be used to construct a personal diploid genome sequence by including personal variants into reference genome. ref
   
 CNVnator a tool for CNV discovery and genotyping from depth of read mapping. ref1ref2
   
 AGE a tool that implements an algorithm for optimal alignment of sequences with SVs.  ref
   
 Belka a software that implements RigidFinder, a method to detect protein rigid blocks from two different conformations.  ref