Filter BED on splice junctions
Filter out lines of a BED file that have junctions that are in in the reference bed file of known junctions. The start position of the exon preceding the junction and the end position of the exon after the junction can be extended. This is to compensate for alignments that may not include enough of the exons surrounding the junctions.
A typical application would be to run tophat twice, once with the --GTF and --no-novel-juncs options for well known splice junctions, then a second time without those options to also include novel splice junctions.
This application would filter out the well splice known junctions from the run intended to find all splice junctions including novel ones.