BWA & GATK parallel parameters.

jofe

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Join Date: Aug 2013

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BWA & GATK parallel parameters.

08-28-2013, 05:44 AM

Hi everybody,
I just want to know if there is some place where I can find technical documentation about how BWA & GATK handle parallelism. I've run some tests and I got some odd results.

I used -t during aln with BWA, -nt RealignerRargetCreator, and -nct with BaseRecalibrator and PrintReads.

For what I understand -t and -nt create threads, one for each core. But do they also allow several threads on one core? Have anyone try this?

Supposedly -nct create several threads within a single core, being 8 the optimal number, according GATK documentation. However I got better results using more. I suspect that uses more core than just one.

Anybody got same results?

Thanks

Jo
Tags: bwa, gatk, parallelism, parameters, thread

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