GATK-DepthOfCoverage: how long should it take

[lre1234]

Hi all,
I am running the GATK depth of coverage tool on a whole genome sample. When I started the analysis, the progress meter showed this:

INFO 08:08:14,491 ProgressMeter - 1:601688 5.90e+05 30.0 s 50.9 s 0.0% 42.9 h 42.9 h

Should this really take 42 hours to run? Or am I misinterpreting the progress meter outputs? Can this be run in a multi-thread fashion, Or would a better approach be to break the file up into smaller pieces and run it by chromosomes, or some other fashion?

Thanks

[vdauwera]

It depends a lot on how you're running it (e.g. whole genome or exome targets only?) and what kind of machine you're running on (e.g. personal computer or server?).

For more details and advice on running GATK tools, visit the GATK documentation website (http://www.broadinstitute.org/gatk/) and ask your questions in the GATK support forum here (http://gatkforums.broadinstitute.org/).