From ff5ac986d8e3146fa5af4df88298f15e216ae42e Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 10 Jan 2013 23:31:46 -0500
Subject: [PATCH] Fix docs for QD

---
 .../sting/gatk/walkers/annotator/QualByDepth.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 4a85e3435..ee4b8910d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -68,7 +68,7 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Variant confidence (from the QUAL field) / unfiltered depth.
+ * Variant confidence (from the QUAL field) / unfiltered depth of non-reference samples.
  *
  * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
  * reads associated with the samples with polymorphic genotypes.