From 2d1e385ca4d9a1137043e7b58bfd3db510173f04 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 7 Nov 2011 14:04:13 -0500
Subject: [PATCH] Adding note to VQSR docs about Rscript being needed in the
 environment PATH.

---
 .../walkers/variantrecalibration/VariantRecalibrator.java     | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 59e0bc530..f60a94a22 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -66,6 +66,10 @@ import java.util.*;
  * the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.
  *
  * <p>
+ * NOTE: In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
+ * See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
+ *
+ * <p>
  * See the GATK wiki for a tutorial and example recalibration accuracy plots.
  * http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration
  *