Deletion detection on seq-cap experiments

[Tom Bair]

Does anyone have any scripts/techniques for finding deletions in a seq-capture experiment. I have never seen more than a single bp deletion in the HCDiff file so I am assuming that they will not show up there. I suspect that I will have to write something to dive into the paired-alignments file to find reads that have a large gap, but wanted to see if anyone else has invented this wheel yet.

Thanks