Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

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?

Comments

Sign In or Register to comment.