I am trying to generate 2 bam files that are the differences between 2 bams using bamutil diff.

http://genome.sph.umich.edu/wiki/BamUtil:_diff#Usage

After trying it for a while, I find it's exaclty what I need, but it's taken a long time (more than 10 hours and running) to compare two human 30x builds:

~/src/bamUtil/bin/bam diff --mapQual --onlyDiffs --recPoolSize 100000 --posDiff 100000 --in1 $bam1 --in2 $bam2 --out onlyDiffs.bam

Any ideas what I can do to speed it up?

https://github.com/statgen/bamUtil/issues/7