this is for breakpointer Partial mis-alignments of short NGS reads in the vicinity of Structural Variants (SVs) is often viewed as a source of artifacts for calling point mutations. I described an algorithm, Breakpointer, to utilize such mis-alignments to inform SV breakpoints. The usage of distribution pattern of read ends can reveal insertions longer than the read or fragment length, as well as breakpoints in repetitive regions, making it a valuable component for an initial scan of possible SV breakpoints.

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads, Bioinformatics, 2012