I wanted to post this question to the GATK support forum, but I can't for the life of me figure out how to do it, so here it goes.
How bad exactly is it to use HaplotypeCallerSpark in GATK 220.127.116.11? I realize it's in beta, but I'm wondering if that means "your results will be useless" or just "use with caution". The reason I'm asking that is because it seems like Spark is the only way to multi-thread in GATK 4.
Here's an example of my usage:
gatk --java-options "-Xmx32g -XX:ParallelGCThreads=1" HaplotypeCallerSpark --spark-master local -R myref.1.2bit -I mybam.bam -O tmygvcf.g.vcf --emit-ref-confidence GVCF --min-dangling-branch-length 1 --min-pruning 1