Hi,
by default SPARK 2 has no support for log4j2. It uses Log4j 1.2.17. When I use GATK 4.0.0 build "as-is" (depends on Log4j2) all jobs on SPARK fail due to version clash. How this is supposed to be solved?
As a workaround I was able:
- relocate Log4j to different package
- make sure it is included in the {{-spark}} jar (it is excluded by default)
But I believe there must be better and cleaner way of running current GATK 4.0.0 on SPARK.
Thanks!