diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index b536eef57..3805e48df 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -396,7 +396,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
             throw new UserException("All samples requested to be included were also requested to be excluded.");
 
-        for ( String sample : samples )
+        if ( ! NO_SAMPLES_SPECIFIED )
+            for ( String sample : samples )
             logger.info("Including sample '" + sample + "'");
 
         // if user specified types to include, add these, otherwise, add all possible variant context types to list of vc types to include
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
index 2afe50982..48c4c8a4f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
@@ -116,8 +116,14 @@ public class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDepende
         }
 
         // create the config offsets
-        for ( final VCFContigHeaderLine contig : header.getContigLines())
-            contigNames.add(contig.getID());
+        if ( ! header.getContigLines().isEmpty() ) {
+            logger.info("Found contig lines in BCF2 file, using those");
+            contigNames.clear();
+            for ( final VCFContigHeaderLine contig : header.getContigLines())
+                contigNames.add(contig.getID());
+        } else {
+            logger.info("Didn't find any contig lines in BCF2 file, falling back (dangerously) to GATK reference dictionary");
+        }
 
         // create the string dictionary
         dictionary = parseDictionary(header);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index 665e0fbff..41621f66e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -64,8 +64,9 @@ class BCF2Writer extends IndexingVariantContextWriter {
     // --------------------------------------------------------------------------------
 
     private final void createContigDictionary(final Collection<VCFContigHeaderLine> contigLines) {
-        for ( final VCFContigHeaderLine contig : contigLines )
-            contigDictionary.put(contig.getID(), contig.getContigIndex());
+        int offset = 0;
+        for ( VCFContigHeaderLine contig : contigLines )
+            contigDictionary.put(contig.getID(), offset++);
     }
 
     @Override