Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include
Additionally, for full details on the leafcutter for Mendelian Diseases (leafcutterMD) method that performs outlier splicing detection, see our Bioinformatics publication.
We have a Google group for user questions at https://groups.google.com/forum/#!forum/leafcutter-users