No plots generated by AnalyzeCovariates in GATK4-Alpha
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?