diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 081192e20..ddd9b1f79 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -10,10 +10,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Map;
+import java.util.*;
 
 
 /**
@@ -256,6 +253,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     /**
      * get the genotype
      *
+     * // todo -- WTF is this?  This is a deeply unsafe call
+     *
      * @return a map in lexigraphical order of the genotypes
      */
     public Genotype getCalledGenotype() {
@@ -301,6 +300,18 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.getSampleNames();
     }
 
+//    public Map<String, Genotype> getSampleGenotypes() {
+//        String[] samples = getSampleNames();
+//        List<Genotype> genotypes = getGenotypes();
+//        HashMap<String, Genotype> map = new HashMap<String, Genotype>();
+//
+//        for ( int i = 0; i < samples.length; i++ ) {
+//            map.put(samples[i], genotypes.get(i));
+//        }
+//
+//        return map;
+//    }
+
     public Map<String, String> getInfoValues() {
         assertNotNull();
         return mCurrentRecord.getInfoValues();
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
index ea9ba4f2a..cd75f2659 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
@@ -4,6 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.Utils;
 
 import java.util.*;
 
@@ -22,7 +23,7 @@ public class ConcordanceTruthTable {
     private static final int FALSE_POSITIVE = 2;
     private static final int FALSE_NEGATIVE = 3;
     private static final int VARIANT = 1;
-    private static final String[] POOL_HEADERS = {"TRUE_POSITIVE","TRUE_NEGATIVE","FALSE_POSITIVE","FALSE_NEGATIVE"};
+    private static final String[] POOL_HEADERS = {"TP","TN","FP","FN"};
 
     private static final int REF = 0;
     private static final int VAR_HET = 1;
@@ -103,24 +104,19 @@ public class ConcordanceTruthTable {
             }
         } else { // if we cannot associate tables with individuals, then we are working in a pooled context
             // first we need to expand our tables to include frequency information
+            Pair<Integer, Pair<Integer,Integer> > poolVariant = getPooledAlleleFrequency(chipEvals, ref);
 
-            Pair<Genotype, Pair<Integer,Integer> > poolVariant = getPooledAlleleFrequency(chipEvals, ref);
-
-            int truthType = getGenotype(poolVariant.getFirst(),ref); // convenience method; now to interpret
-
-            if (truthType == VAR_HET || truthType == VAR_HOM) {
-                truthType = VARIANT;
-            }
-
+            int truthType = poolVariant.getFirst(); // convenience method; now to interpret
             int callType = getCallIndex(eval,ref);
 
             int numTrueSupportingAlleles = poolVariant.getSecond().getFirst();
             if ( numTrueSupportingAlleles > 0 && truthType == VARIANT && callType != VARIANT ) {
-                violation = String.format("False negative: %s with %d alt alleles",
-                        chipEvals.get(0).getFirst(), numTrueSupportingAlleles);
+                violation = String.format("False negative: %s with %d alt alleles", chipEvals.get(0).getFirst(), numTrueSupportingAlleles);
+            } else if ( truthType == REF && callType == VARIANT ) {
+                violation = String.format("False positive: %s at hom-ref site", eval);
             }
 
-            addFrequencyEntry( truthType,callType, poolVariant.getSecond().getFirst() );
+            addFrequencyEntry( truthType, callType, poolVariant.getSecond().getFirst() );
 
         }
 
@@ -131,46 +127,48 @@ public class ConcordanceTruthTable {
         return violation;
     }
 
-    public Pair< Genotype , Pair<Integer,Integer> > getPooledAlleleFrequency( List<Pair<Genotype,Genotype>> chips, char ref) {
-        // TODO -- this is actually just a note that I wanted to appear in blue. This method explicitly uses
-        // TODO --- the assumption that tri-allelic sites do not really exist, and that if they do the
-        // TODO --- site will be marked as such by an 'N' in the reference, so we will not get to this point.
-        Genotype variant = null;
+    public Pair<Integer, Pair<Integer,Integer>> getPooledAlleleFrequency( List<Pair<Genotype,Genotype>> chips, char ref) {
+        // this is actually just a note that I wanted to appear in blue. This method explicitly uses
+        // the assumption that tri-allelic sites do not really exist, and that if they do the
+        // site will be marked as such by an 'N' in the reference, so we will not get to this point.
+
         int frequency = 0;
         int nChips = 0;
         if ( chips != null ) {
             for ( Pair<Genotype,Genotype> chip : chips ) {
                 Genotype c = chip.getFirst();
                 if ( c != null ) {                    
-                    nChips ++;
+                    nChips++;
                     if ( c.isVariant(ref) ) {
                         if ( c.isHet() ) {
-                            frequency ++;
+                            frequency++;
                         } else { // c is hom
                             frequency += 2;
                         }
-                        variant = c;
                     }
+                    //System.out.printf("  Genotype %s at %c => %d%n", c, ref, frequency);
                 }
             }
+            //System.out.printf("*** %d%n", frequency);
         }
 
-        return new Pair< Genotype, Pair<Integer,Integer> >(variant, new Pair<Integer,Integer>(frequency,nChips));
-
+        int truthType = nChips > 0 ? ( frequency > 0 ? VARIANT : REF ) : NO_CALL;
+        return new Pair<Integer, Pair<Integer,Integer> >(truthType, new Pair<Integer,Integer>(frequency,nChips));
     }
 
-    private void addFrequencyEntry ( int truthIndex, int callIndex, int numTrueSupportingAlleles ) {
-        calls_totals[callIndex] ++;
-        truth_totals[truthIndex] ++;
+    private void addFrequencyEntry( int truthIndex, int callIndex, int numTrueSupportingAlleles ) {
+        //System.out.printf(" %s %s %d%n", CALL_NAMES[truthIndex], CALL_NAMES[callIndex], numTrueSupportingAlleles);
+        calls_totals[callIndex]++;
+        truth_totals[truthIndex]++;
 
-        if ( truthIndex == REF && callIndex == REF ) {
+        if ( truthIndex == REF && ( callIndex == REF || callIndex == NO_CALL ) ) {
             // true negative
-            table[numTrueSupportingAlleles][TRUE_NEGATIVE] ++;
+            table[numTrueSupportingAlleles][TRUE_NEGATIVE]++;
             // sanity check - there should never be an entry in
             // [*][TRUE_NEGATIVE] for * > 0
         } else if ( truthIndex == REF && callIndex == VARIANT ) {
             // false positive
-            table[numTrueSupportingAlleles][FALSE_POSITIVE] ++;
+            table[numTrueSupportingAlleles][FALSE_POSITIVE]++;
         } else if ( truthIndex == VARIANT && (callIndex == NO_CALL || callIndex == REF) ) {
             // false negative
             table[numTrueSupportingAlleles][FALSE_NEGATIVE]++;
@@ -224,22 +222,39 @@ public class ConcordanceTruthTable {
             addFrequencyStats(s);
     }
 
-    private void addFrequencyStats(List<String> s) {
+//    private void addFrequencyStats(List<String> s) {
+//
+//        // TODO -- implement me for pooled mode with frequency stats
+//        s.add(String.format("name                 %s",name));
+//        s.add(String.format("TRUTH_ALLELE_FREQUENCY\tERROR_OR_TRUTH_TYPE\tTOTAL\tAS_PRCT_OF_TOTAL_CALLS\tAS_PRCT_OF_CALLS_AT_FREQUENCY"));
+//
+//        for ( int af = 0; af < table.length; af ++ ) {
+//            for ( int errorIndex = 0; errorIndex < 4; errorIndex ++ ) {
+//                StringBuffer sb = new StringBuffer();
+//                sb.append(String.format("%f ", ((double) af)/ table.length));
+//                sb.append(String.format("%s ",POOL_HEADERS[errorIndex]));
+//                sb.append(String.format("%d ", table[af][errorIndex]));
+//                sb.append(String.format("%s ", percentOfTotal(table,af,errorIndex)));
+//                sb.append(String.format("%s ", marginalPercent(table[af],errorIndex)));
+//                s.add(sb.toString());
+//            }
+//        }
+//
+//    }
 
-        // TODO -- implement me for pooled mode with frequency stats
+    private void addFrequencyStats(List<String> s) {
         s.add(String.format("name                 %s",name));
-        s.add(String.format("TRUTH_ALLELE_FREQUENCY\tERROR_OR_TRUTH_TYPE\tTOTAL\tAS_PRCT_OF_TOTAL_CALLS\tAS_PRCT_OF_CALLS_AT_FREQUENCY"));
+        s.add("TRUTH_ALLELE_COUNT\tTRUTH_ALLELE_FREQ\tTOTAL\t" + Utils.join(" ", POOL_HEADERS));
 
         for ( int af = 0; af < table.length; af ++ ) {
+            int sum = 0;
+            String counts = "";
             for ( int errorIndex = 0; errorIndex < 4; errorIndex ++ ) {
-                StringBuffer sb = new StringBuffer();
-                sb.append(String.format("%f ", ((double) af)/ table.length));
-                sb.append(String.format("%s ",POOL_HEADERS[errorIndex]));
-                sb.append(String.format("%d ", table[af][errorIndex]));
-                sb.append(String.format("%s ", percentOfTotal(table,af,errorIndex)));
-                sb.append(String.format("%s ", marginalPercent(table[af],errorIndex)));
-                s.add(sb.toString());
+                int count = table[af][errorIndex];
+                sum += count;
+                counts += String.format(" %6d", count);
             }
+            s.add(String.format("%6d %.3f %6d%s", af, ((double)af)/ table.length, sum, counts));
         }
 
     }
@@ -321,24 +336,4 @@ public class ConcordanceTruthTable {
         sb.append("%");
         return sb.toString();
     }
-
-    private static String percentOfTotal(int [][] errorMatrix, int alleleFrequency, int errorIndex ) {
-        int count = 0;
-        for ( int i = 0; i < errorMatrix.length; i ++ ) {
-            for ( int j = 0; j < 4; j ++ ) {
-                count += errorMatrix[i][j];
-            }
-        }
-
-        return cellPercent(errorMatrix[alleleFrequency][errorIndex], count );
-    }
-
-    private static String marginalPercent ( int[] errors, int errorIndex ) {
-        int count = 0;
-        for ( int i = 0; i < 4; i ++ ) {
-            count += errors[i];
-        }
-
-        return cellPercent(errors[errorIndex], count);
-    }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java
index 71084672b..a9ce647f1 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java
@@ -7,6 +7,6 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
  * Time: 4:39:12 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface PoolAnalysis {
+public interface PoolAnalysis extends PopulationAnalysis, GenotypeAnalysis {
     
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
index 460048636..62ff415e3 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -48,8 +48,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @Argument(fullName="supressDateInformation", doc="This flag indicates that we want to suppress the date information from the output, so that if can be diff'ed against previous evals.", required=false)
     public boolean supressDateInformation = false;
 
-    @Argument(fullName = "numPeopleInPool", shortName="PS", doc="If using a variant file from a pooled caller, this field provides the number of individuals in each pool", required=false)
-    public int numPeopleInPool = -1;
+    //@Argument(fullName = "numPeopleInPool", shortName="PS", doc="If using a variant file from a pooled caller, this field provides the number of individuals in each pool", required=false)
+    //public int numPeopleInPool = -1;
 
     @Argument(fullName = "samplesFile", shortName="samples", doc="When running an analysis on one or more individuals with truth data, this field provides a filepath to the listing of which samples are used (and are used to name corresponding rods with -B)", required=false)
     public String samplesFile = null;
@@ -130,14 +130,16 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
 
         analyses.add(new VariantCounter());
         analyses.add(new VariantDBCoverage(knownSNPDBName));
+
         if ( samplesFile != null ) {
-            if ( numPeopleInPool < 1 )
-                analyses.add(new GenotypeConcordance(samplesFile, true));
-            else
-                analyses.add(new PooledConcordance(samplesFile, true));
+            //if ( numPeopleInPool < 1 )
+            //    analyses.add(new GenotypeConcordance(samplesFile, true));
+            //else
+            analyses.add(new PooledConcordance(samplesFile, true));
         } else {
             analyses.add(new GenotypeConcordance(genotypeChipName, false));
         }
+
         analyses.add(new TransitionTranversionAnalysis());
         analyses.add(new NeighborDistanceAnalysis());
         analyses.add(new HardyWeinbergEquilibrium(badHWEThreshold));
@@ -160,7 +162,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
             } else if ( ! (analysis instanceof PopulationAnalysis || analysis instanceof PoolAnalysis) ) {
                 removed = analysis;
                 iter.remove();
-            } else if ( numPeopleInPool > 1 && ! ( analysis instanceof PoolAnalysis ) ) {
+//            } else if ( numPeopleInPool > 1 && ! ( analysis instanceof PoolAnalysis ) ) {
+            } else if ( analysis instanceof PoolAnalysis && samplesFile == null ) {
                 removed = analysis;
                 iter.remove();
             }