No plots produced by AnalyzeCovariates GATK4Alpha

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created by AmandaChamberlain

on 2017-04-27

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 plots are not produced.

Should this script have been a part of the install?

From slee on 2017-05-02

Hi @AmandaChamberlain,

This looks like a bug—-I’ve filed an issue here: https://github.com/broadinstitute/gatk/issues/2644 Thanks for bringing it to our attention!