diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index fb05a6b04..161179f84 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -27,9 +27,10 @@ package org.broadinstitute.sting.gatk.io.storage;
 import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
+import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
+import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
 import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -81,6 +82,18 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             throw new ReviewedStingException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
     }
 
+    /**
+     * Constructs an object which will redirect into a different file.
+     * @param stub Stub to use when synthesizing file / header info.
+     * @param tempFile File into which to direct the output data.
+     */
+    public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) {
+        logger.debug("Creating temporary output file " + tempFile.getAbsolutePath() + " for VariantContext output.");
+        this.file = tempFile;
+        this.writer = vcfWriterToFile(stub, file, false);
+        writer.writeHeader(stub.getVCFHeader());
+    }
+
     /**
      * common initialization routine for multiple constructors
      * @param stub Stub to use when constructing the output file.
@@ -139,19 +152,6 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         }
     }
 
-
-    /**
-     * Constructs an object which will redirect into a different file.
-     * @param stub Stub to use when synthesizing file / header info.
-     * @param tempFile File into which to direct the output data.
-     */
-    public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) {
-        logger.debug("Creating temporary VCF file " + tempFile.getAbsolutePath() + " for VCF output.");
-        this.file = tempFile;
-        this.writer = vcfWriterToFile(stub, file, false);
-        writer.writeHeader(stub.getVCFHeader());
-    }
-
     public void add(VariantContext vc) {
         writer.add(vc);
     }
@@ -176,12 +176,20 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
 
     public void mergeInto(VariantContextWriterStorage target) {
         try {
-            String sourceFilePath = file.getAbsolutePath();
-            String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
-            logger.debug(String.format("Merging %s into %s",sourceFilePath,targetFilePath));
-            AbstractFeatureReader<VariantContext> source = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
+            final String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
+            logger.debug(String.format("Merging %s into %s",file.getAbsolutePath(),targetFilePath));
+
+            // use the feature manager to determine the right codec for the tmp file
+            // that way we don't assume it's a specific type
+            final FeatureManager.FeatureDescriptor fd = new FeatureManager().getByFiletype(file);
+            if ( fd == null )
+                throw new ReviewedStingException("Unexpectedly couldn't find valid codec for temporary output file " + file);
+
+            final FeatureCodec<VariantContext> codec = fd.getCodec();
+            final AbstractFeatureReader<VariantContext> source =
+                    AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false);
             
-            for ( VariantContext vc : source.iterator() ) {
+            for ( final VariantContext vc : source.iterator() ) {
                 target.writer.add(vc);
             }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
index 6ed889eb6..bea7172ea 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.variantcontext.writer.Options;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.io.OutputStream;
@@ -186,6 +187,9 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
         if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY);
 
+        if ( getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile()) )
+            options.add(Options.FORCE_BCF);
+
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);
     }
 
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 570ca7c1c..67e189d11 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
@@ -149,7 +149,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
             if ( bcfVersion.getMinorVersion() < MIN_MINOR_VERSION )
                 error("BCF2Codec can only process BCF2 files with minor version >= " + MIN_MINOR_VERSION + " but this file has minor version " + bcfVersion.getMinorVersion());
 
-            logger.info("BCF version " + bcfVersion);
+            logger.info("Parsing data stream with BCF version " + bcfVersion);
 
             final int headerSizeInBytes = BCF2Type.INT32.read(inputStream);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
index cf34a8b48..513b9fcb5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
@@ -63,9 +63,8 @@ class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser {
 
     @Override
     public LazyGenotypesContext.LazyData parse(final Object data) {
-        if ( logger.isDebugEnabled() )
-            logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each");
-
+//        if ( logger.isDebugEnabled() )
+//            logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each");
         try {
 
             // load our byte[] data into the decoder
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
index 219daf315..7b8224568 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
@@ -76,7 +76,7 @@ public class BCF2FieldWriterManager {
         if ( map.containsKey(field) )
             throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders");
         map.put(field, writer);
-        logger.info(writer);
+        if ( logger.isDebugEnabled() ) logger.debug(writer);
     }
 
     // -----------------------------------------------------------------
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java
index f23166a02..035aff7d6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java
@@ -84,6 +84,16 @@ public class VariantContextWriterFactory {
         }
     }
 
+    /**
+     * Should we output a BCF file based solely on the name of the file at location?
+     *
+     * @param location
+     * @return
+     */
+    public static boolean isBCFOutput(final File location) {
+        return isBCFOutput(location, EnumSet.noneOf(Options.class));
+    }
+
     public static boolean isBCFOutput(final File location, final EnumSet<Options> options) {
         return options.contains(Options.FORCE_BCF) || (location != null && location.getName().contains(".bcf"));
     }