diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/InsertSizeDistribution.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/InsertSizeDistribution.java
index dcbe4dd13..af6d77099 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/InsertSizeDistribution.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/InsertSizeDistribution.java
@@ -11,13 +11,16 @@ import java.util.List;
  * @author chartl
  */
 public class InsertSizeDistribution extends ValueTest {
+    private final int MAPQ_THRESHOLD = 5;
 
     public boolean usePreviouslySeenReads() { return false; }
 
     public Collection<Number> map(ReadBackedPileup pileup) {
         List<Integer> insertSizes = new ArrayList<Integer>(pileup.size());
         for ( PileupElement e : pileup ) {
-            insertSizes.add(Math.abs(e.getRead().getInferredInsertSize()));
+            if ( e.getMappingQual() >= MAPQ_THRESHOLD ) {
+                insertSizes.add(Math.abs(e.getRead().getInferredInsertSize()));
+            }
         }
 
         return (Collection) insertSizes;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java
index 2fe423c5a..f13b7dd66 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java
@@ -13,13 +13,15 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  */
 public class MateOtherContig extends ProportionTest {
 
+    private final int MAPQ_THRESHOLD = 5;
+
     public boolean usePreviouslySeenReads() { return false; }
 
     public Pair<Number,Number> map(ReadBackedPileup pileup) {
         int tot = 0;
         int otherCon = 0;
         for ( PileupElement e : pileup ) {
-            if ( e.getRead().getReadPairedFlag() ) {
+            if ( e.getRead().getReadPairedFlag() && e.getRead().getMappingQuality() >= MAPQ_THRESHOLD ) {
                 ++tot;
                 if ( ! e.getRead().getMateReferenceIndex().equals(e.getRead().getReferenceIndex()) ) {
                     ++otherCon;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateSameStrand.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateSameStrand.java
index 371e4897b..8e0968e51 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateSameStrand.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateSameStrand.java
@@ -12,12 +12,13 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  * To change this template use File | Settings | File Templates.
  */
 public class MateSameStrand extends ProportionTest {
+    private final int MAPQ_THRESHOLD = 5;
 
     public Pair<Number,Number> map(ReadBackedPileup rbp) {
         int numPairs = 0;
         int mateSameStrand = 0;
         for (PileupElement e : rbp ) {
-            if ( e.getRead().getReadPairedFlag() ) {
+            if ( e.getRead().getReadPairedFlag() && e.getMappingQual() >= MAPQ_THRESHOLD) {
                 ++numPairs;
                 if ( e.getRead().getMateNegativeStrandFlag() == e.getRead().getReadNegativeStrandFlag() ) {
                     ++mateSameStrand;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateUnmapped.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateUnmapped.java
index 70b210ee8..9b0e195d0 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateUnmapped.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateUnmapped.java
@@ -12,12 +12,13 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  * To change this template use File | Settings | File Templates.
  */
 public class MateUnmapped extends ProportionTest {
+    private final int MAPQ_THRESHOLD = 5;
 
     public Pair<Number,Number> map(ReadBackedPileup pileup) {
         int numMatedReads = 0;
         int numPairUnmapped = 0;
         for (PileupElement e : pileup ) {
-            if (e.getRead().getReadPairedFlag()  ) {
+            if (e.getRead().getReadPairedFlag() && e.getMappingQual() >= MAPQ_THRESHOLD ) {
                 ++numMatedReads;
                 if ( e.getRead().getMateUnmappedFlag() ) {
                     ++numPairUnmapped;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ProperPairs.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ProperPairs.java
index 989adfabf..0226841e6 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ProperPairs.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ProperPairs.java
@@ -12,14 +12,17 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  * To change this template use File | Settings | File Templates.
  */
 public class ProperPairs extends ProportionTest {
+    private final int MAPQ_THRESHOLD = 5;
 
     public Pair<Number,Number> map(ReadBackedPileup rbp) {
         int numReads = 0;
         int numPropPair = 0;
         for (PileupElement e : rbp ) {
-            ++numReads;
-            if ( e.getRead().getReadPairedFlag() && e.getRead().getProperPairFlag() ) {
-                ++numPropPair;
+            if ( e.getRead().getReadPairedFlag() && e.getMappingQual() >= MAPQ_THRESHOLD ) {
+                ++numReads;
+                if ( e.getRead().getReadPairedFlag() && e.getRead().getProperPairFlag() ) {
+                    ++numPropPair;
+                }
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsWithIndels.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsWithIndels.java
index d207886a3..eb32b4af0 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsWithIndels.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadsWithIndels.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
+import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -19,8 +20,11 @@ public class ReadsWithIndels extends ProportionTest {
         int numWithIndels = 0;
         for ( PileupElement e : pileup ) {
             ++numReads;
-            if ( e.getRead().getCigar().getCigarElements().contains(CigarOperator.DELETION) || e.getRead().getCigar().getCigarElements().contains(CigarOperator.INSERTION)) {
-                ++numWithIndels;
+            for ( CigarElement element : e.getRead().getCigar().getCigarElements() ) {
+                if ( element.getOperator().equals(CigarOperator.DELETION) || element.getOperator().equals(CigarOperator.INSERTION) ) {
+                    ++numWithIndels;
+                    break;
+                }
             }
         }