diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
index 2a004aaca..66bf562d7 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
@@ -153,9 +153,12 @@ public class CombineReferenceCalculationVariants extends RodWalker<VariantContex
     public void initialize() {
         // take care of the VCF headers
         final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
-        final Set<String> samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
         final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
         headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
+        if ( dbsnp != null && dbsnp.dbsnp.isBound() )
+            VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
+
+        final Set<String> samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
         final VCFHeader vcfHeader = new VCFHeader(headerLines, samples);
         vcfWriter.writeHeader(vcfHeader);
 
@@ -204,7 +207,7 @@ public class CombineReferenceCalculationVariants extends RodWalker<VariantContex
             result = genotypingEngine.calculateGenotypes(result);
 
         // if it turned monomorphic and we don't want such sites, quit
-        if ( !INCLUDE_NON_VARIANTS && result.isMonomorphicInSamples() )
+        if ( result == null || (!INCLUDE_NON_VARIANTS && result.isMonomorphicInSamples()) )
             return null;
 
         // re-annotate it
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 14b5118ad..8f0abe360 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -374,7 +374,7 @@ public abstract class ArgumentTypeDescriptor {
                         FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
                         if ( featureDescriptor != null ) {
                             tribbleType = featureDescriptor.getName();
-                            logger.info("Dynamically determined type of " + file + " to be " + tribbleType);
+                            logger.debug("Dynamically determined type of " + file + " to be " + tribbleType);
                         }
                     }
 
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
index e0b5dd4cb..fbbaa6636 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
@@ -96,7 +96,7 @@ public class IndexDictionaryUtils {
                                                        final ValidationExclusion.TYPE validationExclusionType ) {
         // if the sequence dictionary is empty (as well as null which means it doesn't have a dictionary), skip validation
         if (trackDict == null || trackDict.size() == 0)
-            logger.info("Track " + trackName + " doesn't have a sequence dictionary built in, skipping dictionary validation");
+            logger.warn("Track " + trackName + " doesn't have a sequence dictionary built in, skipping dictionary validation");
         else {
             Set<String> trackSequences = new TreeSet<String>();
             for (SAMSequenceRecord dictionaryEntry : trackDict.getSequences())
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
index 4c50cfaae..a587a3984 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
@@ -34,6 +34,7 @@ import org.broad.tribble.TribbleException;
 import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
 import org.broad.tribble.util.LittleEndianOutputStream;
+import org.broad.tribble.util.TabixUtils;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@@ -169,9 +170,11 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      */
     private Pair<AbstractFeatureReader, SAMSequenceDictionary> createTabixIndexedFeatureSource(FeatureManager.FeatureDescriptor descriptor, String name, File inputFile) {
         // we might not know the index type, try loading with the default reader constructor
-        logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
+        logger.debug("Attempting to load " + inputFile + " as a tabix indexed file without validating it");
         try {
-            return new Pair<AbstractFeatureReader, SAMSequenceDictionary>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null);
+            final File indexFile = new File(inputFile.getAbsoluteFile() + TabixUtils.STANDARD_INDEX_EXTENSION);
+            final SAMSequenceDictionary dict = TabixUtils.getSequenceDictionary(indexFile);
+            return new Pair<>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)), dict);
         } catch (TribbleException e) {
             throw new UserException(e.getMessage(), e);
         }
@@ -318,7 +321,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      * @return an Index, or null if we're unable to load
      */
     protected Index loadFromDisk( final File inputFile, final File indexFile ) {
-        logger.info("Loading Tribble index from disk for file " + inputFile);
+        logger.debug("Loading Tribble index from disk for file " + inputFile);
         Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());
 
         // check if the file is up-to date (filestamp and version check)
@@ -384,7 +387,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      */
     protected Index createIndexInMemory(File inputFile, FeatureCodec codec) {
         // this can take a while, let them know what we're doing
-        logger.info("Creating Tribble index in memory for file " + inputFile);
+        logger.debug("Creating Tribble index in memory for file " + inputFile);
         Index idx = IndexFactory.createDynamicIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
         validateAndUpdateIndexSequenceDictionary(inputFile, idx, dict);
         return idx;
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index e8ce80d07..e1ed63bc0 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -1045,8 +1045,9 @@ public class GATKVariantContextUtils {
      * @return new VariantContext representing the merge of all VCs or null if it not relevant
      */
     public static VariantContext referenceConfidenceMerge(final List<VariantContext> VCs, final GenomeLoc loc, final Byte refBase) {
-
-        if ( VCs == null || VCs.size() == 0 ) throw new IllegalArgumentException("VCs cannot be null or empty");
+        // this can happen if e.g. you are using a dbSNP file that spans a region with no gVCFs
+        if ( VCs == null || VCs.size() == 0 )
+            return null;
 
         // establish the baseline info (sometimes from the first VC)
         final VariantContext first = VCs.get(0);
@@ -1536,6 +1537,8 @@ public class GATKVariantContextUtils {
                                                     final List<Allele> remappedAlleles,
                                                     final List<Allele> targetAlleles) {
         for ( final Genotype g : VC.getGenotypes() ) {
+	    if ( !g.hasPL() )
+		throw new UserException("cannot merge genotypes from samples without PLs; sample " + g.getSampleName() + " does not have likelihoods at position " + VC.getChr() + ":" + VC.getStart());
 
             // only add if the name is new
             final String name = g.getSampleName();