the current version of pindel, v0.2.4, is able to find out and report long insertions. However its user manual didn't note about this. I want to know how it find it, because according to the split reads strategy, it seems impossible.
And according to http://seqanswers.com/forums/showthread.php?t=18083 (#8), using -z option can report the exact inserted sequence. Really?