SOAPsv: is a program for detecting the structural variation
...Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.
This command-line tool will help people who want to compare 2 csv-like files, and get a detailed report on which rows and fields differ between both files. An awk-based version and Perl Version is currently available.