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About java threads in GATK
Since GATK is based on Java, and java is known for spawning multiple threads for many GATK applications like Haplotypecaller, CombineGVCF, GenotypeGVCF, GenomicsDBimport and so on, there are ways to control such thread spawning when you have limited computing resource. In some GATK forums, we have been advised to use -XX:ConcGCThreads and also -XX:ParallelGCThreads. Since their usage requires in-depth understanding of how java multithreading works, it is difficult for me to understand when to use what. Can someone from the GATK developers team explain which -XX method should be used?