diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 7426a7726..b7f71c1ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -240,6 +240,14 @@ public class VariantDataManager {
             if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
                   value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
             }
+	    if (vc.isIndel() && annotationKey.equalsIgnoreCase("QD")) {
+		// normalize QD by event length for indel case
+		int eventLength = Math.abs(vc.getAlternateAllele(0).getBaseString().length() - vc.getReference().getBaseString().length()); // ignore multi-allelic complication here for now
+		    if (eventLength > 0) // sanity check
+			value /= (double)eventLength;
+
+	    }
+
             if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
             if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
         } catch( Exception e ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index c9b63878d..2afa315ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -67,6 +67,9 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
     protected String sampleName = null;
 
+    @Argument(fullName="fixRef", shortName="fixRef", doc="Fix common reference base in case there's an indel without padding", required=false)
+    protected boolean fixReferenceBase = false;
+
     private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
     private boolean wroteHeader = false;
 
@@ -104,6 +107,10 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                 vc = VariantContext.modifyGenotypes(vc, genotypes);
             }
 
+            // todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
+            if (fixReferenceBase) {
+                vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
+            }
             writeRecord(vc, tracker, ref.getBase());
         }