From fc890b6e45af3c1fcf6f8adb1d7a5ababeadce8b Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Sun, 3 May 2015 01:04:49 +0200
Subject: [PATCH] Moved MQ0 out of HC exclusion and into StandardUGAnnotation

---
 .../tools/walkers/annotator/MappingQualityZeroBySample.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
index 13057381e6..728fa3fa31 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
@@ -50,7 +50,7 @@
  * <p>This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
  *
  * <h3>Caveat</h3>
- * <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
+ * <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
  *
  * <h3>Related annotations</h3>
  * <ul>