I wander why the mulitple thread parameter [-nt ] has been cancer in GATK4.0? Or GATK 4.0 use a better way to replace the mulitple threads process, like using Spark?
I asked the same question. Please take a look at this thread:
The Spark version is still in beta and is not recommended for production use. We probably have to wait for a while.
Some of the newer tools in GATK4 use spark natively and are fully functional (like the CNV tools). For the "classic" germline tools like HwplotypeCaller, the team is actively working on evaluating and finalizing the spark implementations. We are aware that there is significant demand for this feature and are working hard to deliver it in the near future, at least for the most popular tools like HaplotypeCaller.
For anyone interested in this topic: see the updated doc on parallelism and the new doc on Spark.