Question: Bamutil Diff Speed Ups?
0
gravatar for 14134125465346445
5.4 years ago by
United Kingdom
141341254653464453.4k wrote:

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

tools bam • 1.2k views
ADD COMMENTlink modified 5.4 years ago by Pierre Lindenbaum113k • written 5.4 years ago by 141341254653464453.4k
1
gravatar for Pierre Lindenbaum
5.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum113k wrote:

split your two BAMs by chromosome , and run "bam diff" on each subset ?

ADD COMMENTlink written 5.4 years ago by Pierre Lindenbaum113k
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