diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index a9a7de75f..71e65f2fb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -44,6 +44,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
+import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
@@ -686,10 +687,22 @@ public class GenomeAnalysisEngine {
         for (ReadFilter filter : filters)
             filter.initialize(this);
 
-        sampleDB = new SampleDB(getSAMFileHeader(), argCollection.sampleFiles);
-
         // set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference
         rodDataSources = getReferenceOrderedDataSources(referenceMetaDataFiles,referenceDataSource.getReference().getSequenceDictionary(),genomeLocParser,argCollection.unsafe);
+
+        // set up sample db
+        initializeSampleDB();
+    }
+
+    /**
+     * Entry-point function to initialize the samples database from input data and pedigree arguments
+     */
+    private void initializeSampleDB() {
+        SampleDBBuilder sampleDBBuilder = new SampleDBBuilder(this, argCollection.pedigreeValidationType);
+        sampleDBBuilder.addSamplesFromSAMHeader(getSAMFileHeader());
+        sampleDBBuilder.addSamplesFromSampleNames(SampleUtils.getUniqueSamplesFromRods(this));
+        sampleDBBuilder.addSamplesFromPedigreeArgument(argCollection.pedigreeData);
+        sampleDB = sampleDBBuilder.getFinalSampleDB();
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java
index 33bed89d2..fd42a24f4 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java
@@ -56,8 +56,12 @@ public class SampleDBBuilder {
     /**
      * Hallucinates sample objects for all the samples in the SAM file and stores them
      */
-    public SampleDBBuilder addSamples(SAMFileHeader header) {
-        for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
+    public SampleDBBuilder addSamplesFromSAMHeader(final SAMFileHeader header) {
+        return addSamplesFromSampleNames(SampleUtils.getSAMFileSamples(header));
+    }
+
+    public SampleDBBuilder addSamplesFromSampleNames(final Collection<String> sampleNames) {
+        for (final String sampleName : sampleNames) {
             if (sampleDB.getSample(sampleName) == null) {
                 final Sample newSample = new Sample(sampleName, sampleDB);
                 addSample(newSample);
@@ -66,7 +70,7 @@ public class SampleDBBuilder {
         return this;
     }
 
-    public SampleDBBuilder addSamples(final List<String> pedigreeArguments) {
+    public SampleDBBuilder addSamplesFromPedigreeArgument(final List<String> pedigreeArguments) {
         for (final String ped : pedigreeArguments) {
             final File pedFile = new File(ped);
             if ( pedFile.exists() )
@@ -105,6 +109,7 @@ public class SampleDBBuilder {
      * @param sample to be added
      */
     protected SampleDBBuilder addSample(Sample sample) {
+        // todo -- merge with existing record if we have one
         sampleDB.addSample(sample);
         return this;
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
index 57bc6cf3b..e63fc7feb 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
@@ -299,7 +299,6 @@ public class PedReaderUnitTest extends BaseTest {
             super(PedReaderTestTagParsing.class);
             this.tags = tags;
             this.expected = missingDesc;
-
         }
     }