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No plots generated by AnalyzeCovariates in GATK4-Alpha

AmandaChamberlainAmandaChamberlain Agriculture VictoriaMember

I'm using GATK4-Alpha AnalyzeCovariates

java -Xmx80G -jar $GATK AnalyzeCovariates -before recal.table -after after_recal.table -plots recal_plots.pdf

The tool appears to finish however I then get an error referring to an R script

java.lang.IllegalArgumentException: Resource not found relative to class org.broadinstitute.hellbender.utils.recalibration.RecalUtils: BQSR.R

and now plots are produced.

Should this script have been a part of the install?

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