diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 4e7bef808..41f522eea 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -42,7 +42,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
@@ -114,8 +113,13 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         else
             indelLength = vc.getAlternateAllele(0).length();
 
+        if ( indelLength > 200 ) {
+            writer.add(vc, ref.getBase());
+            return 0;
+        }
+
         // create an indel haplotype
-        int originalIndex = (int)(ref.getLocus().getStart() - ref.getWindow().getStart()) + 1;
+        int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
         final byte[] originalIndel = makeHaplotype(vc, refSeq, originalIndex, indelLength);
 
         // create a CIGAR string to represent the event
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 8478b2d65..34dcd7d54 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -52,16 +52,16 @@ public class UnifiedArgumentCollection {
     public boolean ALL_BASES_MODE = false;
 
     @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called", required = false)
-    public double STANDARD_CONFIDENCE_FOR_CALLING = 50.0;
+    public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
 
     @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false)
-    public double STANDARD_CONFIDENCE_FOR_EMITTING = 50.0;
+    public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
 
     @Argument(fullName = "trigger_min_confidence_threshold_for_calling", shortName = "trig_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be called", required = false)
-    public double TRIGGER_CONFIDENCE_FOR_CALLING = 50.0;
+    public double TRIGGER_CONFIDENCE_FOR_CALLING = 30.0;
 
     @Argument(fullName = "trigger_min_confidence_threshold_for_emitting", shortName = "trig_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false)
-    public double TRIGGER_CONFIDENCE_FOR_EMITTING = 50.0;
+    public double TRIGGER_CONFIDENCE_FOR_EMITTING = 30.0;
 
     @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
     public boolean NO_SLOD = false;