diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index e542460c5..aaac7c765 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -19,7 +19,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         executeTest("testHaplotypeCaller: args=" + args, spec);
     }
 
-    @Test
+    //@Test
     public void testHaplotypeCallerMultiSample() {
         HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c");
     }
@@ -81,4 +81,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing AD for reduced reads
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Test
+    public void HCtestADAnnotationInReducedBam() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
+                Arrays.asList("6ac31dbea0ffc289b6feadb47457d427"));    //TODO: once the HC is fixed, update MD5
+        executeTest("HC test AD Annotation when calling on a ReducedRead BAM", spec);
+    }
+
+
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index d1b86fdf2..d7790969e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -73,7 +73,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         ReadBackedPileup pileup = stratifiedContext.getBasePileup();
         for ( PileupElement p : pileup ) {
             if ( alleleCounts.containsKey(p.getBase()) )
-                alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
+                alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+p.getRepresentativeCount());
         }
 
         // we need to add counts in the correct order
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index e95af71c2..c4fae5d5b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -275,7 +275,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             for (PileupElement p : sample.getValue().getBasePileup()) {
-                if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
+//                if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
+                if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions
                     continue;
 
                 if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider )
@@ -290,7 +291,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                     int row = matchesRef ? 0 : 1;
                     int column = isFW ? 0 : 1;
 
-                    table[row][column]++;
+                    table[row][column]+=p.getRepresentativeCount();
                 }
             }
         }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index f3fe63e95..b61ce5571 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -438,4 +438,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
         executeTest("test calling on reads with Ns in CIGAR", spec);
     }
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing AD for reduced reads
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Test
+    public void testADAnnotationInReducedBam() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
+                Arrays.asList("84486c88a0fd1ae996a6402490db8492"));
+        executeTest("test AD Annotation when calling on a ReducedRead BAM", spec);
+    }
+
 }