Setup

leafcutter requires regtools to be installed for the initial pre-processing.

The actual leafcutter program will be run on Docker using https://hub.docker.com/r/francois4/leafcutter.

Running

Start by following the instructions here: http://davidaknowles.github.io/leafcutter/articles/Usage.html

Depending on the sample, you might get an error like the following when running the leafcutter_cluster_regtools.py step:

current = E[0]
IndexError: list index out of range

Follow this step to fix this issue: https://github.com/davidaknowles/leafcutter/issues/176#issuecomment-841301578

Make sure to also use the -checkchrom flag when running the clustering.