Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
On newer versions of gcc, the build fails due to
error: call of overloaded ‘abs(unsigned int)’ is ambiguousPlease see below for a full log:
pindel-error.txt