Pararellization in GATK 4

Pararellization in GATK 4


Hi all,

I’m trying (and failing) to multi-thread HaplotypeCaller in GATK 4. I read in a few places online that multi-threading in GATK 4 has been made more tricky, maybe even unfeasible, but all the places where I read that seem to be more than 1 yr old. Is there a new solution to that problem?

PS: I’ve read in a few places about Spark, but I still don’t have no idea what it is or how to use it.

Here’s what I have at this point:

   java -Xmx16g -XX:ParallelGCThreads=1 -jar gatk-package- HaplotypeCaller -R myfasta.fasta -I mybam.bam -O mygvcf.g.vcf --emit-ref-confidence GVCF --min-dangling-branch-length 1 --min-pruning 1 --num_cpu_threads_per_data_thread 2

A USER ERROR has occurred: num_cpu_threads_per_data_thread is not a recognized option





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