diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java
index 3d32b1ea4..271b57961 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java
@@ -77,8 +77,7 @@ import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 import htsjdk.variant.variantcontext.VariantContextUtils;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
-
+import htsjdk.variant.variantcontext.writer.SortingVariantContextWriter;
 import java.util.*;
 
 /**
@@ -186,7 +185,7 @@ public class HaplotypeResolver extends RodWalker<Integer, Integer> {
             headerLines.add(new VCFInfoHeaderLine(STATUS_KEY, 1, VCFHeaderLineType.String, "Extent to which records match"));
         final VCFHeader vcfHeader = new VCFHeader(headerLines, Collections.<String>emptySet());
         baseWriter.writeHeader(vcfHeader);
-        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, ACTIVE_WINDOW);
+        writer = new SortingVariantContextWriter(baseWriter, ACTIVE_WINDOW);
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java
index 19928c3fd..767d3a103 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java
@@ -81,7 +81,7 @@ import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.SortingVariantContextWriter;
 
 import java.io.*;
 import java.util.*;
@@ -257,7 +257,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
            But, NOTE that map() is careful to pass out a list of records to be written that FIRST includes any records discarded due to having reached mostDownstreamLocusReached,
            and only THEN records located at mostDownstreamLocusReached.  The opposite order in map() would violate the startDistance limits imposed when contracting SortingVCFWriter with (2 * cacheWindow).
          */
-        writer = VariantContextWriterFactory.sortOnTheFly(writer, 2 * cacheWindow, writer != origWriter);
+        writer = new SortingVariantContextWriter(writer, 2 * cacheWindow, writer != origWriter);
 
         // setup the header fields:
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java
index b3f76fe2f..7187e78c5 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java
@@ -38,7 +38,7 @@ import htsjdk.variant.bcf2.BCF2Utils;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFHeader;
 
 import java.io.*;
@@ -82,8 +82,11 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         else if ( stub.getOutputStream() != null ) {
             this.file = null;
             this.stream = stub.getOutputStream();
-            writer = VariantContextWriterFactory.create(stream,
-                    stub.getMasterSequenceDictionary(), stub.getWriterOptions(false));
+            writer = new VariantContextWriterBuilder()
+                    .setOutputVCFStream(stream)
+                    .setReferenceDictionary(stub.getMasterSequenceDictionary())
+                    .setOptions(stub.getWriterOptions(false))
+                    .build();
         }
         else
             throw new ReviewedGATKException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
@@ -131,22 +134,31 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             throw new UserException.CouldNotCreateOutputFile(file, "Unable to open target output stream", ex);
         }
 
-        EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
-        VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
+        final VariantContextWriterBuilder.OutputType fileOutputType = allowCompressed && stub.isCompressed() ?
+                VariantContextWriterBuilder.OutputType.BLOCK_COMPRESSED_VCF : VariantContextWriterBuilder.OutputType.VCF;
+        final EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
+
+        VariantContextWriter writer = new VariantContextWriterBuilder()
+                        .setOutputFile(file)
+                        .setOutputFileType(fileOutputType)
+                        .setReferenceDictionary(stub.getMasterSequenceDictionary())
+                        .setIndexCreator(stub.getIndexCreator())
+                        .setOptions(options)
+                        .build();
 
         // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
         // TODO -- remove me when argument generateShadowBCF is removed
-        if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
+        if ( stub.alsoWriteBCFForTest() &&
+                ! (options.contains(Options.FORCE_BCF) || file != null && file.getName().contains(".bcf")) ) {
             final File bcfFile = BCF2Utils.shadowBCF(file);
             if ( bcfFile != null ) {
-                FileOutputStream bcfStream;
-                try {
-                    bcfStream = new FileOutputStream(bcfFile);
-                } catch (FileNotFoundException e) {
-                    throw new RuntimeException(bcfFile + ": Unable to create BCF writer", e);
-                }
+                final VariantContextWriter bcfWriter = new VariantContextWriterBuilder()
+                        .setOutputFile(bcfFile)
+                        .setOutputFileType(VariantContextWriterBuilder.OutputType.BCF)
+                        .setReferenceDictionary(stub.getMasterSequenceDictionary())
+                        .setOptions(options)
+                        .build();
 
-                VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, bcfStream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
                 writer = new TestWriter(writer, bcfWriter);
             }
         }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java
index 6cd63497a..276b5c309 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java
@@ -34,7 +34,6 @@ import org.broadinstitute.gatk.engine.GATKVCFUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
 
@@ -216,7 +215,8 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( indexOnTheFly) options.add(Options.INDEX_ON_THE_FLY);
         if ( writeFullFormatField ) options.add(Options.WRITE_FULL_FORMAT_FIELD);
 
-        if ( forceBCF || (getOutputFile() != null && VariantContextWriterFactory.isBCFOutput(getOutputFile())) )
+        final File file = getOutputFile();
+        if ( forceBCF || (file != null && options.contains(Options.FORCE_BCF) || file != null && file.getName().contains(".bcf")) )
             options.add(Options.FORCE_BCF);
 
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
index 65936795c..f361cfa33 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
@@ -51,7 +51,7 @@ import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextComparator;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 
 import java.io.*;
 import java.util.*;
@@ -265,11 +265,16 @@ public class CatVariants extends CommandLineProgram {
             }
         }
 
-        FileOutputStream outputStream = new FileOutputStream(outputFile);
         EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
         IndexCreator idxCreator = GATKVCFUtils.makeIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
-        final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
 
+        final VariantContextWriter outputWriter =
+                new VariantContextWriterBuilder()
+                        .setOutputFile(outputFile)
+                        .setReferenceDictionary(ref.getSequenceDictionary())
+                        .setIndexCreator(idxCreator)
+                        .setOptions(options)
+                        .build();
         boolean firstFile = true;
         int count = 0;
         while(!priorityQueue.isEmpty() ){
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index c169a2844..7d24bdd5a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -55,7 +55,7 @@ import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.SortingVariantContextWriter;
 
 import java.util.*;
 
@@ -194,7 +194,7 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
 
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
 
-        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, MAX_INDEL_LENGTH);
+        writer = new SortingVariantContextWriter(baseWriter, MAX_INDEL_LENGTH);
 
         referenceWindowStop = getToolkit().getArguments().reference_window_stop;
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
index ce737178a..5e50a3a97 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
@@ -44,7 +44,7 @@ import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 
 import java.io.File;
 import java.util.*;
@@ -134,14 +134,20 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         if(splitToMany){
             writers = new VariantContextWriter[numOfFiles];
             for(int i = 0; i<writers.length; i++){
-                writers[i] = VariantContextWriterFactory.create(new File(baseFileName+".split."+i+".vcf"), getMasterSequenceDictionary());
+                writers[i] = new VariantContextWriterBuilder()
+                                .setOutputFile(new File(baseFileName+".split."+i+".vcf"))
+                                .setReferenceDictionary(getMasterSequenceDictionary())
+                                .build();
                 writers[i].writeHeader(new VCFHeader(hInfo,samples));
             }
 
         }
         else {
             vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
-            vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
+            vcfWriter2 = new VariantContextWriterBuilder()
+                            .setOutputFile(file2)
+                            .setReferenceDictionary(getMasterSequenceDictionary())
+                            .build();
             vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
         }
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
index 7a316cbb5..e1624fa4a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
@@ -41,7 +41,7 @@ import org.broadinstitute.gatk.engine.GATKVCFUtils;
 import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.SortingVariantContextWriter;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
 
@@ -100,7 +100,7 @@ public class VariantsToAllelicPrimitives extends RodWalker<Integer, Integer> {
 
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
 
-        vcfWriter = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
+        vcfWriter = new SortingVariantContextWriter(baseWriter, 200);
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
index 3bf2c11b5..a2a55d69b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
@@ -52,7 +52,7 @@ import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.SortingVariantContextWriter;
 
 import java.io.File;
 import java.util.*;
@@ -116,7 +116,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     VariantOverlapAnnotator variantOverlapAnnotator = null;
 
     public void initialize() {
-        vcfwriter = VariantContextWriterFactory.sortOnTheFly(baseWriter, 40, false);
+        vcfwriter = new SortingVariantContextWriter(baseWriter, 40);
         variantOverlapAnnotator = new VariantOverlapAnnotator(dbsnp.dbsnp, getToolkit().getGenomeLocParser());
     }