diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
index eb59bac9e..78e34f136 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
@@ -144,4 +144,9 @@ public interface AllelicVariant extends ReferenceOrderedDatum {
     /** returns the length of the variant.  For SNPs this is just 1.
      */
     int length();
+
+    /**
+     * returns TRUE if the variant is one for pooled calls, FALSE if it is not
+     */
+    boolean isPooled();
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
index d3f44faa0..36f4ebc1b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
@@ -46,6 +46,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
+    public boolean isPooled() { return true; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return Integer.parseInt(this.get("EM_N")); }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
index a0d88f002..b54b6f46a 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
@@ -407,5 +407,10 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         }
         return glf;
     }
+
+    @Override
+    public boolean isPooled() {
+        return false;
+    }
 }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
index b83d510a3..bcfa43aeb 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
@@ -171,6 +171,8 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
         return true;
     }
 
+    public boolean isPooled() { return false; }
+
     public int length() { return 1; }
 
     public char getReferenceBase() { return refBase; }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
index 3f8107700..f0f1f036b 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
@@ -175,4 +175,5 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
     public int length() { return 1; }
+    public boolean isPooled() { return false; }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
index 3e71e0457..22c98546e 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
@@ -32,6 +32,7 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
+    public boolean isPooled() { return false; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return -1; }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
index 85579645d..ef4279a0d 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
@@ -58,6 +58,7 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
     public double getHeterozygosity() { return 0.0; }
     public double getMAF() { return 0.0; }
     public int getPloidy() { return 2; }
+    public boolean isPooled() { return false; }
     public int length() {
         if ( is1KGFormat() )
              return Integer.parseInt(this.get("2"));
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index dc01c9cfb..874fd5908 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -239,4 +239,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 	}
 
     public int length() { return (int)(loc.getStop() - loc.getStart() + 1); }
+
+    public boolean isPooled() { return false; }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
new file mode 100755
index 000000000..3806d5f11
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
@@ -0,0 +1,152 @@
+package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.LinkedList;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: Sep 9, 2009
+ * Time: 4:45:21 PM
+ * To change this template use File | Settings | File Templates.
+ *
+public class PooledGenotypeConcordance extends BasicVariantAnalysis implements GenotypeAnalysis {
+    private String[][] individualsByPool = null;
+    private int nPools;
+
+    private static final int REF = 0;
+    private static final int VAR_SINGLE = 1;
+    private static final int VAR_MULTI = 2;
+    private static final int UNKNOWN = 3;
+    private static final int NO_CALL = 3;   // synonym
+    private static final String[] TRUTH_NAMES = {"IS_REF", "IS_SINGLE_VARIANT", "IS_MULTIPLE_VARIANT", "UNKNOWN"};
+    private static final String[] CALL_NAMES = {"CALLED_REF", "CALLED_SINGLE_VARIANT", "CALLED_MULTIPLE_VARIANT", "NO_CALL"};
+    // todo -- consider the resolution: single vs multi enough, or should there be deeper resolution?
+
+    private int[][][] table;
+    private int[][] truthTotalsByPool;
+    private int[][] callTotalsByPool;
+
+    public PooledGenotypeConcordance(String pathToHapmapPoolFile) {
+        super("genotype_concordance");
+        BufferedReader fileReader = null;
+        try {
+        fileReader = new BufferedReader(new FileReader(pathToHapmapPoolFile));
+        } catch (IOException e) {
+            String errorMsg = "Could not open any file at " + pathToHapmapPoolFile + " Please check to see if the path is accurate.";
+            throw new StingException(errorMsg, e);
+        }
+
+        generateNameTableFromFile(fileReader);
+
+        truthTotalsByPool = new int[nPools][4];
+        callTotalsByPool = new int[nPools][4];
+        table = new int[nPools][4][4];
+        for(int pool = 0; pool < nPools; pool++) {
+            for(int call1 = 0; call1 < 4; call1++) {
+                for(int call2 = 0; call2 < 4; call2++)
+                {
+                    table[pool][call1][call2] = 0;
+                }
+                callTotalsByPool[pool][call1] = 0;
+                truthTotalsByPool[pool][call1] = 0;
+            }
+        }
+
+    }
+
+    public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context){
+        for(int pool = 0; pool < nPools; pool ++) {
+            incorporatePoolCall(eval, tracker, ref, context, pool);
+        }
+
+        return null;
+    }
+
+    public void incorporatePoolCall(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context, int pool) {
+        for( int nameOffset = 0; nameOffset < individualsByPool[pool].length; nameOffset++) {
+            inc(eval, tracker, ref, context, pool, nameOffset);
+        }
+    }
+
+    public void inc(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context, int pool, int nameOffset) {
+        AllelicVariant chip = (AllelicVariant) tracker.lookup(individualsByPool[pool][nameOffset],null);
+
+    }
+
+
+     //
+     // private methods for reading names into individualsByPool from an external file
+     //
+
+    private void generateNameTableFromFile(BufferedReader reader) {
+        // first line is a special case
+        String firstline;
+        if(continueReading(reader)) {
+            firstline = readLine(reader);
+        } else {
+            String errMsg = "First line of the HapmapPoolFile " + reader.toString() + " could not be read. Please check that the path and file properly formatted.";
+            throw new StingException(errMsg);
+        }
+
+        StringTokenizer tokFirstLine = new StringTokenizer(firstline);
+        nPools = tokFirstLine.countTokens();
+        LinkedList<String>[] namesByPool = new LinkedList[nPools];
+
+        for( int firstLineIterator = 0; firstLineIterator < nPools; firstLineIterator ++) {
+            namesByPool[firstLineIterator] = new LinkedList();
+            namesByPool[firstLineIterator].add(tokFirstLine.nextToken());
+        }
+
+        while(continueReading(reader)) {
+            String line = readLine(reader);
+            StringTokenizer tokLine = new StringTokenizer(line);
+            int newNames = tokLine.countTokens();
+            for(int lineIt = 0; lineIt < newNames; lineIt ++ ) {
+                namesByPool[lineIt].add(tokLine.nextToken());
+            }
+        }
+
+        convertListOfNamesToMatrix(namesByPool);
+    }
+
+    private boolean continueReading(BufferedReader reader) {
+        boolean continueReading = false;
+        try {
+            continueReading = reader.ready();
+        } catch(IOException e) {
+            continueReading = false;
+        }
+        return continueReading;
+    }
+
+    private String readLine(BufferedReader reader) {
+        String line;
+        try {
+            line = reader.readLine();
+        } catch( IOException e) {
+            String errMsg = "BufferedReader pointing to "+reader.toString()+" was declared ready but no line could be read from it.";
+            throw new StingException(errMsg,e);
+        }
+        return line;
+    }
+
+    private void convertListOfNamesToMatrix(LinkedList<String>[] names) {
+        // initialize matrix
+        for( int pool = 0; pool < nPools; pool ++) {
+            individualsByPool[pool] = new String[names[pool].size()];
+            individualsByPool[pool] = names[pool].toArray(individualsByPool[pool]);
+        }
+
+    }
+}
+*/
\ No newline at end of file
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 e22aa896d..8b3bd115e 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
@@ -58,6 +58,9 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @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 = "pathToHapmapPoolFile", shortName="HPF", doc="If using a variant file from a pooled caller on pools of hapmap individuals, this field provides a filepath to the pool construction file listing which hapmap individuals are in which pool", required=false)
+    public String pathToHapmapPoolFile = null;
+
     String analysisFilenameBase = null;
 
     final String knownSNPDBName = "dbSNP";