BWA & GATK parallel parameters.

[jofe]

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