Pindel on Helix
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.
If you use the program frequently, it may be convenient to add the program directory to your path.
For a single session:
$ PATH=/usr/local/pindel:$PATH; export PATH (bash)
To add this directory to your path at login time automatically, add the appropriate line above to the end of your ~/.cshrc or ~/.bashrc file.
How To Use
$ pindel command 1
$ pindel command 2