Question: Bamutil Diff Speed Ups?
gravatar for 14134125465346445
5.0 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.

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?

tools bam • 1.1k views
ADD COMMENTlink modified 5.0 years ago by Pierre Lindenbaum107k • written 5.0 years ago by 141341254653464453.4k
gravatar for Pierre Lindenbaum
5.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k wrote:

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

ADD COMMENTlink written 5.0 years ago by Pierre Lindenbaum107k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 708 users visited in the last hour