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What is status of multithreading in GATK 3.4?

dhfxdhfx Austin, TXMember

I am running GATK 3.4.0-g7e26428 on a 64-bit 8-core 16-thread Linux system, using a test case of 5 million paired short reads on chr15 of the human genome to extrapolate the full-genome timing for HaplotypeCaller. For the 5 million pairs, without the -nct option I get ~ 26 minutes; with -nct 8 it's ~ 20 minutes. My Java version is OpenJDK 64-Bit Server VM 1.7.0_79-b14. I would expect more like a x8 speedup; why am I not seeing that?

HaplotypeCaller does not appear to accept the -nt option. Is there any way (besides farming out the individual chromosomes) to run multiple data threads?

Thanks in advance for any helpful advice.

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