chunkbam

Documentation

Overview

chunkbam accepts a bam file and the number of regions to split it into and outputs BED of intervals split evenly by number of reads. This is useful for parallelization. It can process a 7GB RNA-Seq file (note that this will have very uneven coverage) in about 1 minute, 25 seconds of user time with 20 CPUs. It starts outputting rows ready for parallelization in < 5 seconds.