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-18.104.22.168-local.jar 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