arq5x/lumpy-sv — pull request #46 by cc2qe (2014-12-09 15:57:28+00:00)
Title: Ignore proper pair flag in generating insert size distribution

In some libraries, the "unbiased" insert size distribution (ignoring proper pair flag from the aligner) is different from the proper pairs distribution. This is especially relevant when a library contains a subset of fragments with smaller insert size
![insert_size_unbiased_proper_compare](https://cloud.githubusercontent.com/assets/3903682/5360003/1a1e43ce-7f87-11e4-96b5-cda5391d9cea.png)

In these cases, LUMPY over-reports small deletions because it expects a much narrower insert size distribution than the true distribution, resulting in a large number of small (< 50 bp), false positive deletion calls.
![na12883_deletion_size](https://cloud.githubusercontent.com/assets/3903682/5360101/c898de78-7f87-11e4-8349-f7ff171490fa.png)

These small false positive deletions disappear with this pull request. It's also possible (although yet untested) that they will improve performance on mate-pair libraries (https://github.com/arq5x/lumpy-sv/issues/45) (as these often have a subset of small fragments)
![na12883_unbiased](https://cloud.githubusercontent.com/assets/3903682/5360140/0ac93202-7f88-11e4-9fb1-bc410f4e84fa.png)

NB: The outlier discarding is a clone of Travis's commit: https://github.com/arq5x/lumpy-sv/commit/00463ad8546c8efeb84a892625c157078f2dc103