From 4e7ecbdcb2b23093275c9a48205ac4c44c74c841 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 22 May 2011 16:44:12 +0000
Subject: [PATCH] FS values need to be jittered just like HRun

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5835 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/VariantDataManager.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 92b733a35..a66413bb4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -207,7 +207,7 @@ public class VariantDataManager {
 
     private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter ) {
         double value;
-        if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // HRun values must be jittered a bit to work in this GMM
+        if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM
             value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
             value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
         } else if( annotationKey.equals("QUAL") ) {