diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
index 5bc02c6c3..27150e5de 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFGenotypeWriterStorage.java
@@ -51,11 +51,18 @@ public class VCFGenotypeWriterStorage extends GenotypeWriterStorage<VCFGenotypeW
         ((VCFGenotypeWriter)writer).addRecord(vcfRecord);    
     }
 
+    /**
+     * set the validation stringency
+     * @param value   validation stringency value
+     */
+    public void setValidationStringency(VALIDATION_STRINGENCY value) {
+        ((VCFGenotypeWriter)writer).setValidationStringency(value);
+    }
+
     /**
      * Merges the stream backing up this temporary storage into the target.
      * @param target Target stream for the temporary storage.  May not be null.
      */
-    @Override
     public void mergeInto(VCFGenotypeWriter target) {
         VCFReader reader = new VCFReader(file);
         while ( reader.hasNext() )
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
index c2abdfe00..75ca245e8 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
@@ -50,4 +50,12 @@ public class VCFGenotypeWriterStub extends GenotypeWriterStub<VCFGenotypeWriter>
     public void addRecord(VCFRecord vcfRecord) {
         outputTracker.getStorage(this).addRecord(vcfRecord);
     }
+
+    /**
+     * set the validation stringency
+     * @param value   validation stringency value
+     */
+    public void setValidationStringency(VALIDATION_STRINGENCY value) {
+        outputTracker.getStorage(this).setValidationStringency(value);
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 6362cb03b..2e70fe6da 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -100,7 +100,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
         if ( UAC.POOLSIZE < 1 && UAC.genotypeModel == GenotypeCalculationModel.Model.POOLED ) {
             throw new IllegalArgumentException("Attempting to use the POOLED model with a pool size less than 1. Please set the pool size to an appropriate value.");
         }
-        if ( UAC.LOD_THRESHOLD > Double.MIN_VALUE ) {
+        if ( UAC.LOD_THRESHOLD != Double.MIN_VALUE ) {
             StringBuilder sb = new StringBuilder();
             sb.append("\n***\tThe --lod_threshold argument is no longer supported; instead, please use --min_confidence_threshold.");
             sb.append("\n***\tThere is approximately a 10-to-1 mapping from confidence to LOD.");
@@ -108,7 +108,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             throw new IllegalArgumentException(sb.toString());
         }
 
-        // some arguments can't be handled (for now) while we are multi-threaded
+        // some arguments can't be handled (at least for now) while we are multi-threaded
         if ( getToolkit().getArguments().numberOfThreads > 1 ) {
             // no ASSUME_SINGLE_SAMPLE because the IO system doesn't know how to get the sample name
             if ( UAC.ASSUME_SINGLE_SAMPLE != null )
@@ -118,6 +118,13 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
                 throw new IllegalArgumentException("For technical reasons, the VERBOSE argument cannot be used with multiple threads");
         }
 
+        // set up the writer manually if it needs to use the output stream
+        if ( writer == null && out != null ) {
+            logger.warn("For technical reasons, VCF format must be used when writing to standard out.");
+            logger.warn("Specify an output file if you would like to use a different output format.");
+            writer = GenotypeWriterFactory.create(GenotypeWriterFactory.GENOTYPE_FORMAT.VCF, out);
+        }
+
         // get all of the unique sample names - unless we're in POOLED mode, in which case we ignore the sample names
         if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED ) {
             // if we're supposed to assume a single sample, do so
@@ -130,11 +137,15 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             //     logger.debug("SAMPLE: " + sample);
         }
 
-        // set up the writer manually if it needs to use the output stream
-        if ( writer == null && out != null ) {
-            logger.warn("For technical reasons, VCF format must be used when writing to standard out.");
-            logger.warn("Specify an output file if you would like to use a different output format.");
-            writer = GenotypeWriterFactory.create(GenotypeWriterFactory.GENOTYPE_FORMAT.VCF, out);
+        // in pooled mode we need to check that the format is acceptable
+        if ( UAC.genotypeModel == GenotypeCalculationModel.Model.POOLED && writer != null ) {
+            // only multi-sample calls use Variations
+            if ( !writer.supportsMultiSample() )
+                throw new IllegalArgumentException("The POOLED model is not compatible with the specified format; try using VCF instead");
+
+            // when using VCF with multiple threads, we need to turn down the validation stringency so that writing temporary files will work
+            if ( getToolkit().getArguments().numberOfThreads > 1 && writer instanceof VCFGenotypeWriter )
+                ((VCFGenotypeWriter)writer).setValidationStringency(VCFGenotypeWriterAdapter.VALIDATION_STRINGENCY.SILENT);
         }
 
         // initialize the verbose writer
@@ -175,10 +186,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
 
         // annotation (INFO) fields from UnifiedGenotyper
         headerInfo.add(new VCFHeaderLine("INFO_NOTE", "\"All annotations in the INFO field are generated only from the FILTERED context used for calling variants\""));
-        headerInfo.add(new VCFInfoHeaderLine("AF", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
-        headerInfo.add(new VCFInfoHeaderLine("NS", 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
+        headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
+        headerInfo.add(new VCFInfoHeaderLine(VCFRecord.SAMPLE_NUMBER_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
         if ( !UAC.NO_SLOD )
-            headerInfo.add(new VCFInfoHeaderLine("SB", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));
+            headerInfo.add(new VCFInfoHeaderLine(VCFRecord.STRAND_BIAS_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));
 
         // FORMAT fields if not in POOLED mode
         if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED )
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriter.java
index d82d6c5ce..1c19b77a3 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriter.java
@@ -25,4 +25,12 @@ public interface VCFGenotypeWriter extends GenotypeWriter {
      * @param vcfRecord Record to add.
      */
     public void addRecord(VCFRecord vcfRecord);    
+
+    /**
+     * set the validation stringency
+     * @param value   validation stringency value
+     */
+    public void setValidationStringency(VALIDATION_STRINGENCY value);
+    
+    public enum VALIDATION_STRINGENCY { STRICT, SILENT };
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
index fe9a5be63..7b77b793f 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
@@ -16,14 +16,18 @@ import java.util.*;
  *         Adapt the VCF writter to the genotype output system
  */
 public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
+
     // our VCF objects
     private VCFWriter mWriter = null;
     private VCFHeader mHeader = null;
     private final Set<String> mSampleNames = new LinkedHashSet<String>();
 
-    /** our log, which we want to capture anything from this class */
+    // our log, which we want to capture anything from this class
     protected static Logger logger = Logger.getLogger(VCFGenotypeWriterAdapter.class);
 
+    // validation stringency
+    private VALIDATION_STRINGENCY validationStringency = VALIDATION_STRINGENCY.STRICT;
+
 
     public VCFGenotypeWriterAdapter(File writeTo) {
         if (writeTo == null) throw new RuntimeException("VCF output file must not be null");
@@ -41,7 +45,6 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
      * @param sampleNames  the sample names
      * @param headerInfo  the optional header fields
      */
-    @Override
     public void writeHeader(Set<String> sampleNames, Set<VCFHeaderLine> headerInfo) {
         mSampleNames.addAll(sampleNames);
 
@@ -96,7 +99,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
         // get the location and reference
         if ( genotypes.size() == 0 ) {
             if ( locusdata == null )
-                throw new IllegalArgumentException("Unable to parse out the current location: genotype array must contain at least one entry or have locusdata");
+                throw new IllegalArgumentException("Unable to parse out the current location: genotype array must contain at least one entry or have variation data");
 
             params.setLocations(locusdata.getLocation(), locusdata.getReference().charAt(0));
 
@@ -121,7 +124,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
             }
         }
 
-        if (genotypeMap.size() > 0) {
+        if ( validationStringency == VALIDATION_STRINGENCY.STRICT && genotypeMap.size() > 0 ) {
             for (String name : genotypeMap.keySet())
                 logger.fatal("Genotype " + name + " was present in the VCFHeader");
             throw new IllegalArgumentException("Genotype array passed to VCFGenotypeWriterAdapter contained Genotypes not in the VCF header");
@@ -151,11 +154,11 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
                                             params.getFormatString(),
                                             params.getGenotypesRecords());
 
-        mWriter.addRecord(vcfRecord);
+        mWriter.addRecord(vcfRecord, validationStringency);
     }
 
     public void addRecord(VCFRecord vcfRecord) {
-        mWriter.addRecord(vcfRecord);
+        mWriter.addRecord(vcfRecord, validationStringency);
     }
 
     /**
@@ -227,4 +230,11 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
         return map;
     }
 
+    /**
+     * set the validation stringency
+     * @param value   validation stringency value
+     */
+    public void setValidationStringency(VALIDATION_STRINGENCY value) {
+        validationStringency = value;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index b28a59dfe..fc9752629 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -504,6 +504,17 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
      * @return a string
      */
     public String toStringEncoding(VCFHeader header) {
+        return toStringEncoding(header, VCFGenotypeWriter.VALIDATION_STRINGENCY.STRICT);
+    }
+
+    /**
+     * the generation of a string representation, which is used by the VCF writer
+     *
+     * @param header                the VCF header for this VCF Record
+     * @param validationStringency  the validation stringency
+     * @return a string
+     */
+    public String toStringEncoding(VCFHeader header, VCFGenotypeWriter.VALIDATION_STRINGENCY validationStringency) {
         StringBuilder builder = new StringBuilder();
 
         // CHROM \t POS \t ID \t REF \t ALT \t QUAL \t FILTER \t INFO
@@ -524,9 +535,15 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         builder.append(FIELD_SEPERATOR);
         builder.append(createInfoString());
 
-        if (this.hasGenotypeData()) {
-            addGenotypeData(builder, header);
+        if ( this.hasGenotypeData() ) {
+            try {
+                addGenotypeData(builder, header);
+            } catch (Exception e) {
+                if ( validationStringency == VCFGenotypeWriter.VALIDATION_STRINGENCY.STRICT )
+                    throw new RuntimeException(e.getMessage());
+            }
         }
+
         return builder.toString();
     }
 
@@ -553,28 +570,31 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
      * @param header  the header object
      */
     private void addGenotypeData(StringBuilder builder, VCFHeader header) {
-        builder.append(FIELD_SEPERATOR + mGenotypeFormatString);
-        if (header.getGenotypeSamples().size() < getGenotypes().size())
-            throw new RuntimeException("We have more genotype samples than the header specified");
+        StringBuffer tempStr = new StringBuffer();
+        if ( header.getGenotypeSamples().size() < getGenotypes().size() )
+            throw new IllegalStateException("We have more genotype samples than the header specified");
+        tempStr.append(FIELD_SEPERATOR + mGenotypeFormatString);
 
         Map<String, VCFGenotypeRecord> gMap = genotypeListToMap(getGenotypes());
         String[] genotypeFormatStrings = mGenotypeFormatString.split(":");
 
-        for (String genotype : header.getGenotypeSamples()) {
-            builder.append(FIELD_SEPERATOR);
-            if (gMap.containsKey(genotype)) {
+        for ( String genotype : header.getGenotypeSamples() ) {
+            tempStr.append(FIELD_SEPERATOR);
+            if ( gMap.containsKey(genotype) ) {
                 VCFGenotypeRecord rec = gMap.get(genotype);
-                builder.append(rec.toStringEncoding(this.mAlts, genotypeFormatStrings));
+                tempStr.append(rec.toStringEncoding(this.mAlts, genotypeFormatStrings));
                 gMap.remove(genotype);
             } else {
-                builder.append(VCFGenotypeRecord.EMPTY_GENOTYPE);
+                tempStr.append(VCFGenotypeRecord.EMPTY_GENOTYPE);
             }
         }
-        if (gMap.size() != 0) {
-            for (String sample : gMap.keySet())
+        if ( gMap.size() != 0 ) {
+            for ( String sample : gMap.keySet() )
                 System.err.println("Sample " + sample + " is being genotyped but isn't in the header.");
-            throw new RuntimeException("We failed to use all the genotype samples; there must be an inconsistancy between the header and records");
+            throw new IllegalStateException("We failed to use all the genotype samples; there must be an inconsistancy between the header and records");
         }
+
+        builder.append(tempStr);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
index a0187f567..b6c2e56da 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
@@ -84,10 +84,20 @@ public class VCFWriter {
      * @param record the record to output
      */
     public void addRecord(VCFRecord record) {
+        addRecord(record, VCFGenotypeWriter.VALIDATION_STRINGENCY.STRICT);
+    }
+
+    /**
+     * output a record to the VCF file
+     *
+     * @param record                the record to output
+     * @param validationStringency  the validation stringency
+     */
+    public void addRecord(VCFRecord record, VCFGenotypeWriter.VALIDATION_STRINGENCY validationStringency) {
         if ( mHeader == null )
             throw new IllegalStateException("The VCF Header must be written before records can be added");
 
-        String vcfString = record.toStringEncoding(mHeader);
+        String vcfString = record.toStringEncoding(mHeader, validationStringency);
         try {
             mWriter.write(vcfString + "\n");
             mWriter.flush();  // necessary so that writing to an output stream will work