After merging with Yossi's fix I can confirm that the AD is fixed when going through the HC too. Added similar fixes to DP and FS annotations too.

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -83,16 +83,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     // --------------------------------------------------------------------------------------------------------------
     //
-    // testing AD for reduced reads
+    // testing reduced reads
     //
     // --------------------------------------------------------------------------------------------------------------
 
     @Test
-    public void HCtestADAnnotationInReducedBam() {
+    public void HCTestReducedBam() {
         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
+                Arrays.asList("864abe729828248333aee14818c1d2e1"));
-        executeTest("HC test AD Annotation when calling on a ReducedRead BAM", spec);
+        executeTest("HC calling on a ReducedRead BAM", spec);
     }
 
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -49,8 +50,12 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
             if ( perReadAlleleLikelihoodMap.size() == 0 )
                 return null;
 
-            for ( Map.Entry<String, PerReadAlleleLikelihoodMap> sample : perReadAlleleLikelihoodMap.entrySet() )
+            for (PerReadAlleleLikelihoodMap maps : perReadAlleleLikelihoodMap.values() ) {
-                depth += sample.getValue().getNumberOfStoredElements();
+                for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
+                    final GATKSAMRecord read = el.getKey();
+                    depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
+                }
+            }
         }
         else
             return null;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -71,7 +72,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
         }
         else if (stratifiedPerReadAlleleLikelihoodMap != null) {
             // either SNP with no alignment context, or indels: per-read likelihood map needed
-            final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
+            final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc);
             return pValueForBestTable(table, null);
         }
         else
@@ -235,14 +236,13 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
      *   allele2   #       #
      * @return a 2x2 contingency table
      */
-    private static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
+    private static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap, final VariantContext vc) {
-                                                final Allele ref, final Allele alt) {
+        final Allele ref = vc.getReference();
+        final Allele alt = vc.getAltAlleleWithHighestAlleleCount();
         int[][] table = new int[2][2];
 
         for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
             for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
-                if ( el.getKey().isReducedRead() ) // ignore reduced reads
-                    continue;
                 final boolean matchesRef = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(ref,true);
                 final boolean matchesAlt = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(alt,true);
 
@@ -254,7 +254,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                 int row = matchesRef ? 0 : 1;
                 int column = isFW ? 0 : 1;
 
-                table[row][column]++;
+                final GATKSAMRecord read = el.getKey();
+                table[row][column] += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
             }
         }
 
@@ -275,7 +276,6 @@ 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) ) // ignore deletions
                     continue;
 
@@ -291,7 +291,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                     int row = matchesRef ? 0 : 1;
                     int column = isFW ? 0 : 1;
 
-                    table[row][column]+=p.getRepresentativeCount();
+                    table[row][column] += p.getRepresentativeCount();
                 }
             }
         }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -438,18 +438,19 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
         executeTest("test calling on reads with Ns in CIGAR", spec);
     }
+
     // --------------------------------------------------------------------------------------------------------------
     //
-    // testing AD for reduced reads
+    // testing reduced reads
     //
     // --------------------------------------------------------------------------------------------------------------
 
     @Test
-    public void testADAnnotationInReducedBam() {
+    public void testReducedBam() {
         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);
+        executeTest("test calling on a ReducedRead BAM", spec);
     }
 
 }