I'm upgrading a somatic variant calling pipeline from GATK3 to GATK4, and I see that multithreading is no longer a BQSR option in GATK4. The recommended approach appears to be BQSRPipelineSpark, which is still in beta.
Can someone at the Broad clarify the meaning of "beta" here? Is it in beta because of Spark issues and potential crashes, for example, or because the output may be incorrect?
What is the current best practice for parallelizing BQSR?
Thanks in advance!
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