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Could Intel GKL used in GATK4 pipeline HaplotypecallerSpark?

GraceZouGraceZou ChinaMember

We can run HaplotypecallerSpark to get a normal output by using GATK4, but we find although the log shows that "libgkl_pairhmm_omp.so" is loaded, but when we debug the code, we find that the GKL is not used.

we analyse the code and find the following function is not return , could you tell us why this function not return "regionAndIntervals"?

THX.

Issue · Github
by Sheila

Issue Number
3102
State
open
Last Updated
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