Find overlapping junctions

The perl script findOverlappingJunctions.pl uses the CGA Tools function junctionDiff to identify structural variants that are shared in common between two genomes. This is accomplished by removing junctions that differ between the genomes, from the original list of junctions. Any junctions that are output from junctionDiff are by definition different; therefore, removing these from the original SV junction list will find SV overlapping junctions.

Download the tool here.