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Second run of BaseRecalibrator in parallel with HaplotypeCaller
Dear GATK team,
I'd like to ask a question about the possibility of HaplotypeCaller and AnalyzeCovariates running in parallel: I developed a QScript that runs indel realignment, BQSR, variant calling (obtaining gVCF file as a result) and then -- BaseRecalibrator for the second time followed by AnalyzeCovariates. Looking in QScript jobreport PDF file I noticed that the second run of BaseRecalibrator was performed after HaplotypeCaller, though as I can understand, HaplotypeCaller and the second run of BaseRecalibrator are independent regarding data and potentially can run in paralle.
Can I run them in parallel somehow in order to save time?