diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index b001b62d8..5fcd3af6a 100644
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
@@ -98,7 +99,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             engine.setWalker(walker);
             walker.setToolkit(engine);
 
-            Collection<SamRecordFilter> filters = engine.createFilters();
+            Collection<ReadFilter> filters = engine.createFilters();
             engine.setFilters(filters);
 
             // load the arguments into the walker / filters.
@@ -108,7 +109,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             loadArgumentsIntoObject(walker);
             argumentSources.add(walker);
 
-            for (SamRecordFilter filter: filters) {
+            for (ReadFilter filter: filters) {
                 loadArgumentsIntoObject(filter);
                 argumentSources.add(filter);
             }
@@ -186,8 +187,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         walker.setToolkit(engine);
         argumentSources.add(walker.getClass());
 
-        Collection<SamRecordFilter> filters = engine.createFilters();
-        for(SamRecordFilter filter: filters)
+        Collection<ReadFilter> filters = engine.createFilters();
+        for(ReadFilter filter: filters)
             argumentSources.add(filter.getClass());
 
         Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 199f4fff3..154250d01 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -49,8 +49,8 @@ import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
-import org.broadinstitute.sting.gatk.filters.SamRecordHeaderFilter;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -65,7 +65,6 @@ import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
 import java.io.File;
@@ -139,7 +138,7 @@ public class GenomeAnalysisEngine {
     /**
      * Collection of the filters applied to the input data.
      */
-    private Collection<SamRecordFilter> filters;
+    private Collection<ReadFilter> filters;
 
     /**
      * A currently hacky unique name for this GATK instance
@@ -269,8 +268,8 @@ public class GenomeAnalysisEngine {
      * the caller must handle that directly.
      * @return A collection of available filters.
      */
-    public Collection<SamRecordFilter> createFilters() {
-        Set<SamRecordFilter> filters = new HashSet<SamRecordFilter>();
+    public Collection<ReadFilter> createFilters() {
+        Set<ReadFilter> filters = new HashSet<ReadFilter>();
         filters.addAll(WalkerManager.getReadFilters(walker,this.getFilterManager()));
         if (this.getArguments().readGroupBlackList != null && this.getArguments().readGroupBlackList.size() > 0)
             filters.add(new ReadGroupBlackListFilter(this.getArguments().readGroupBlackList));
@@ -733,9 +732,8 @@ public class GenomeAnalysisEngine {
 
         sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
 
-        for (SamRecordFilter filter : filters)
-            if (filter instanceof SamRecordHeaderFilter)
-                ((SamRecordHeaderFilter)filter).setHeader(this.getSAMFileHeader());
+        for (ReadFilter filter : filters)
+            filter.initialize(this);
 
         sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
 
@@ -1020,7 +1018,7 @@ public class GenomeAnalysisEngine {
      * Gets the list of filters employed by this engine.
      * @return Collection of filters (actual instances) used by this engine.
      */
-    public Collection<SamRecordFilter> getFilters() {
+    public Collection<ReadFilter> getFilters() {
         return this.filters;
     }
 
@@ -1028,7 +1026,7 @@ public class GenomeAnalysisEngine {
      * Sets the list of filters employed by this engine.
      * @param filters Collection of filters (actual instances) used by this engine.
      */
-    public void setFilters(Collection<SamRecordFilter> filters) {
+    public void setFilters(Collection<ReadFilter> filters) {
         this.filters = filters;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
index 47af69fa7..1a361029a 100755
--- a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
+++ b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
@@ -6,6 +6,7 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
 import java.util.Collection;
@@ -33,7 +34,7 @@ public class ReadProperties {
     private Integer readBufferSize = null;
     private DownsamplingMethod downsamplingMethod = null;
     private ValidationExclusion exclusionList = null;
-    private Collection<SamRecordFilter> supplementalFilters = null;
+    private Collection<ReadFilter> supplementalFilters = null;
     private boolean includeReadsWithDeletionAtLoci = false;
     private boolean useOriginalBaseQualities = false;
     private boolean generateExtendedEvents = false;
@@ -115,7 +116,7 @@ public class ReadProperties {
         return exclusionList;
     }
 
-    public Collection<SamRecordFilter> getSupplementalFilters() {
+    public Collection<ReadFilter> getSupplementalFilters() {
         return supplementalFilters;
     }
 
@@ -172,7 +173,7 @@ public class ReadProperties {
            Integer readBufferSize,
            DownsamplingMethod downsamplingMethod,
            ValidationExclusion exclusionList,
-           Collection<SamRecordFilter> supplementalFilters,
+           Collection<ReadFilter> supplementalFilters,
            boolean includeReadsWithDeletionAtLoci,
            boolean generateExtendedEvents,
            BAQ.CalculationMode cmode,
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 21ce28173..9553f651e 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -29,6 +29,7 @@ import net.sf.picard.filter.SamRecordFilter;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
@@ -322,9 +323,9 @@ public class WalkerManager extends PluginManager<Walker> {
      * @param filterManager Manages the creation of filters.
      * @return A non-empty list of filters to apply to the reads.
      */
-    public static List<SamRecordFilter> getReadFilters(Class<? extends Walker> walkerClass, FilterManager filterManager) {
-        List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
-        for(Class<? extends SamRecordFilter> filterType: getReadFilterTypes(walkerClass))
+    public static List<ReadFilter> getReadFilters(Class<? extends Walker> walkerClass, FilterManager filterManager) {
+        List<ReadFilter> filters = new ArrayList<ReadFilter>();
+        for(Class<? extends ReadFilter> filterType: getReadFilterTypes(walkerClass))
             filters.add(filterManager.createFilterByType(filterType));
         return filters;
     }
@@ -335,7 +336,7 @@ public class WalkerManager extends PluginManager<Walker> {
      * @param filterManager Manages the creation of filters.
      * @return A non-empty list of filters to apply to the reads.
      */
-    public static List<SamRecordFilter> getReadFilters(Walker walker, FilterManager filterManager) {
+    public static List<ReadFilter> getReadFilters(Walker walker, FilterManager filterManager) {
         return getReadFilters(walker.getClass(), filterManager);
     }
 
@@ -444,8 +445,8 @@ public class WalkerManager extends PluginManager<Walker> {
      * @param walkerClass Class of the walker to inspect.
      * @return An array of types extending from SamRecordFilter.  Will never be null.
      */
-    public static Collection<Class<? extends SamRecordFilter>> getReadFilterTypes(Class<?> walkerClass) {
-        List<Class<? extends SamRecordFilter>> filterTypes = new ArrayList<Class<? extends SamRecordFilter>>();
+    public static Collection<Class<? extends ReadFilter>> getReadFilterTypes(Class<?> walkerClass) {
+        List<Class<? extends ReadFilter>> filterTypes = new ArrayList<Class<? extends ReadFilter>>();
         while(walkerClass != null) {
             if(walkerClass.isAnnotationPresent(ReadFilters.class)) {
                 for ( Class c : walkerClass.getAnnotation(ReadFilters.class).value() ) {
@@ -463,7 +464,7 @@ public class WalkerManager extends PluginManager<Walker> {
      * @param walker The walker to inspect.
      * @return An array of types extending from SamRecordFilter.  Will never be null.
      */
-    public static Collection<Class<? extends SamRecordFilter>> getReadFilterTypes(Walker walker) {
+    public static Collection<Class<? extends ReadFilter>> getReadFilterTypes(Walker walker) {
         return getReadFilterTypes(walker.getClass());
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index ecfe15de7..7a4c632c7 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -33,6 +33,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.iterators.*;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.ReadMetrics;
@@ -146,7 +147,7 @@ public class SAMDataSource {
                 null,
                 null,
                 new ValidationExclusion(),
-                new ArrayList<SamRecordFilter>(),
+                new ArrayList<ReadFilter>(),
                 false,
                 false,
                 false);
@@ -163,7 +164,7 @@ public class SAMDataSource {
             Integer readBufferSize,
             DownsamplingMethod downsamplingMethod,
             ValidationExclusion exclusionList,
-            Collection<SamRecordFilter> supplementalFilters,
+            Collection<ReadFilter> supplementalFilters,
             boolean includeReadsWithDeletionAtLoci,
             boolean generateExtendedEvents,
             boolean enableLowMemorySharding) {
@@ -209,7 +210,7 @@ public class SAMDataSource {
             Integer readBufferSize,
             DownsamplingMethod downsamplingMethod,
             ValidationExclusion exclusionList,
-            Collection<SamRecordFilter> supplementalFilters,
+            Collection<ReadFilter> supplementalFilters,
             boolean includeReadsWithDeletionAtLoci,
             boolean generateExtendedEvents,
             BAQ.CalculationMode cmode,
@@ -632,7 +633,7 @@ public class SAMDataSource {
                                                         StingSAMIterator wrappedIterator,
                                                         Double downsamplingFraction,
                                                         Boolean noValidationOfReadOrder,
-                                                        Collection<SamRecordFilter> supplementalFilters,
+                                                        Collection<ReadFilter> supplementalFilters,
                                                         BAQ.CalculationMode cmode,
                                                         BAQ.QualityMode qmode,
                                                         IndexedFastaSequenceFile refReader,
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/DownsamplerBenchmark.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/DownsamplerBenchmark.java
index 931a04b2d..94b1c2025 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/DownsamplerBenchmark.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/DownsamplerBenchmark.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -78,7 +79,7 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
                                                                0,
                                                                downsampling.create(),
                                                                new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
-                                                               Collections.<SamRecordFilter>emptyList(),
+                                                               Collections.<ReadFilter>emptyList(),
                                                                false,
                                                                false,
                                                                BAQ.CalculationMode.OFF,
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/GATKWalkerBenchmark.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/GATKWalkerBenchmark.java
index e9b75005c..1719f85e6 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/GATKWalkerBenchmark.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/GATKWalkerBenchmark.java
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
@@ -88,7 +89,7 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark {
             engine.setArguments(argCollection);
             // Bugs in the engine mean that this has to be set twice.
             engine.setSAMFileIDs(Collections.singletonList(new SAMReaderID(inputFile,new Tags())));
-            engine.setFilters(Collections.<SamRecordFilter>singletonList(new UnmappedReadFilter()));
+            engine.setFilters(Collections.<ReadFilter>singletonList(new UnmappedReadFilter()));
             engine.setReferenceMetaDataFiles(Collections.<RMDTriplet>emptyList());
 
             // Create the walker
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
index d3e20909f..b8a3ee977 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
@@ -34,7 +34,7 @@ import net.sf.samtools.*;
  * @version 0.1
  */
 
-public class BadCigarFilter implements SamRecordFilter {
+public class BadCigarFilter extends ReadFilter {
 
     public boolean filterOut(final SAMRecord rec) {
         Cigar c = rec.getCigar();
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
index 43dc6a6de..3b988c8fb 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
@@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
  * @version 0.1
  */
 
-public class BadMateFilter implements SamRecordFilter {
+public class BadMateFilter extends ReadFilter {
 
     public boolean filterOut(final SAMRecord rec) {
         return hasBadMate(rec);
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
index aa5a75396..84390c173 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
@@ -42,7 +42,7 @@ import org.broadinstitute.sting.gatk.ReadMetrics;
 public class CountingFilteringIterator implements CloseableIterator<SAMRecord> {
     private final ReadMetrics runtimeMetrics;
     private final Iterator<SAMRecord> iterator;
-    private final Collection<SamRecordFilter> filters;
+    private final Collection<ReadFilter> filters;
     private SAMRecord next = null;
 
     /**
@@ -52,7 +52,7 @@ public class CountingFilteringIterator implements CloseableIterator<SAMRecord> {
      * @param iterator  the backing iterator
      * @param filters    the filter (which may be a FilterAggregator)
      */
-    public CountingFilteringIterator(ReadMetrics metrics, Iterator<SAMRecord> iterator, Collection<SamRecordFilter> filters) {
+    public CountingFilteringIterator(ReadMetrics metrics, Iterator<SAMRecord> iterator, Collection<ReadFilter> filters) {
         this.runtimeMetrics = metrics;
         this.iterator = iterator;
         this.filters = filters;
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
index 241291cd4..fb3c38582 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
@@ -36,7 +36,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out duplicate reads.
  */
 
-public class DuplicateReadFilter implements SamRecordFilter {
+public class DuplicateReadFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getDuplicateReadFlag();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
index 872cba05c..b7806524a 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
@@ -35,7 +35,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out FailsVendorQualityCheck reads.
  */
 
-public class FailsVendorQualityCheckReadFilter implements SamRecordFilter {
+public class FailsVendorQualityCheckReadFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getReadFailsVendorQualityCheckFlag();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
index 3bf11c0ac..cda08fb66 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
@@ -39,9 +39,9 @@ import java.util.Collection;
  * @author mhanna
  * @version 0.1
  */
-public class FilterManager extends PluginManager<SamRecordFilter> {
+public class FilterManager extends PluginManager<ReadFilter> {
     public FilterManager() {
-        super(SamRecordFilter.class,"filter","Filter");
+        super(ReadFilter.class,"filter","Filter");
     }
 
     /**
@@ -50,11 +50,11 @@ public class FilterManager extends PluginManager<SamRecordFilter> {
      * @param filterType The type of the filter
      * @return The filter
      */
-    public SamRecordFilter createFilterByType(Class<? extends SamRecordFilter> filterType) {
+    public ReadFilter createFilterByType(Class<? extends ReadFilter> filterType) {
         return this.createByName(getName(filterType));
     }
 
-    public Collection<Class<? extends SamRecordFilter>> getValues() {
+    public Collection<Class<? extends ReadFilter>> getValues() {
         return this.getPlugins();
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index d56b8b780..4deeb09ee 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
@@ -36,12 +35,12 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
  * @author mhanna
  * @version 0.1
  */
-public class MalformedReadFilter implements SamRecordHeaderFilter {
+public class MalformedReadFilter extends ReadFilter {
     private SAMFileHeader header;
     
     @Override
-    public void setHeader(SAMFileHeader header) {
-        this.header = header;
+    public void initialize(GenomeAnalysisEngine engine) {
+        this.header = engine.getSAMFileHeader();
     }
 
     public boolean filterOut(SAMRecord read) {
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
index d6ebcf487..bcd473b15 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * @version 0.1
  */
 
-public class MappingQualityReadFilter implements SamRecordFilter {
+public class MappingQualityReadFilter extends ReadFilter {
 
     @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
     public int MIN_MAPPING_QUALTY_SCORE = 10;
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
index 48f12de40..8a2fd5af3 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
@@ -35,7 +35,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * @author mhanna
  * @version 0.1
  */
-public class MaxReadLengthFilter implements SamRecordFilter {
+public class MaxReadLengthFilter extends ReadFilter {
     @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required=true)
     private int maxReadLength;
     
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
index 88e09f989..d5d40ec38 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
@@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
  * @version 0.1
  */
 
-public class MissingReadGroupFilter implements SamRecordFilter {
+public class MissingReadGroupFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return rec.getReadGroup() == null;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
index 67fd275c4..fc21538e8 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
@@ -35,7 +35,7 @@ import net.sf.samtools.SAMRecord;
  *
  * Filter out reads that don't have Original Quality scores inside. 
  */
-public class NoOriginalQualityScoresFilter implements SamRecordFilter {
+public class NoOriginalQualityScoresFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return (read.getAttribute("OQ") == null);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
index cbbd4a315..cfbba0383 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
@@ -35,7 +35,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out duplicate reads.
  */
 
-public class NotPrimaryAlignmentReadFilter implements SamRecordFilter {
+public class NotPrimaryAlignmentReadFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getNotPrimaryAlignmentFlag();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
index f8a1c502a..dcddebd55 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
  * @version 0.1
  */
 
-public class Platform454Filter implements SamRecordFilter {
+public class Platform454Filter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (ReadUtils.is454Read(rec));
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
index 710699ae2..691fd95f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * @author ebanks
  * @version 0.1
  */
-public class PlatformFilter implements SamRecordFilter {
+public class PlatformFilter extends ReadFilter {
     @Argument(fullName = "PLFilterName", shortName = "PLFilterName", doc="Discard reads with RG:PL attribute containing this strign", required=false)
     protected String[] PLFilterNames;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
index 6d134794a..4ef88402d 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
@@ -16,7 +16,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
  * Time: 2:54:23 PM
  * To change this template use File | Settings | File Templates.
  */
-public class PlatformUnitFilter implements SamRecordFilter {
+public class PlatformUnitFilter extends ReadFilter {
     // a hack: use static in order to be able to fill it with the data from command line at runtime
     static private Set<String> blackListedLanes = new HashSet<String>();
 
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SamRecordHeaderFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
similarity index 54%
rename from java/src/org/broadinstitute/sting/gatk/filters/SamRecordHeaderFilter.java
rename to java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
index 548115b58..1d74ee20e 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/SamRecordHeaderFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
@@ -2,14 +2,15 @@ package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 /**
  * A SamRecordFilter that also depends on the header.
  */
-public interface SamRecordHeaderFilter extends SamRecordFilter {
+public abstract class ReadFilter implements SamRecordFilter {
     /**
      * Sets the header for use by this filter.
-     * @param header the header for use by this filter.
+     * @param engine the engine.
      */
-    void setHeader(SAMFileHeader header);
+    public void initialize(GenomeAnalysisEngine engine) {}
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
index 965fca0dd..69ebc8b04 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
@@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
  *   PU:1000G-mpimg-080821-1_1
  * would filter out a read with the read group PU:1000G-mpimg-080821-1_1
  */
-public class ReadGroupBlackListFilter implements SamRecordFilter {
+public class ReadGroupBlackListFilter extends ReadFilter {
     private Set<Entry<String, Collection<String>>> filterEntries;
 
     public ReadGroupBlackListFilter(List<String> blackLists) {
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
index 174a0d94b..1b2a77f45 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
@@ -35,7 +35,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * @author chartl
  * @version 0.1
  */
-public class ReadStrandFilter implements SamRecordFilter {
+public class ReadStrandFilter extends ReadFilter {
     @Argument(fullName = "filterPositive", shortName = "fp", doc="Discard reads on the forward strand",required=false)
 	boolean filterForward = false;
     
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
index 7019fed13..682b22b1f 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.Set;
 
-public class SampleFilter implements SamRecordFilter {
+public class SampleFilter extends ReadFilter {
     @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true)
     private Set SAMPLES_TO_KEEP = null;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
index 639ef1486..05b472036 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
@@ -38,7 +38,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * Only use reads from the specified read group.
  */
 
-public class SingleReadGroupFilter implements SamRecordFilter {
+public class SingleReadGroupFilter extends ReadFilter {
     @Argument(fullName = "read_group_to_keep", shortName = "goodRG", doc="The name of the read group to keep, filtering out all others", required=true)
     private String READ_GROUP_TO_KEEP = null;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
index fe6dfbb9e..ac4f4853a 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
@@ -35,7 +35,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out duplicate reads.
  */
 
-public class UnmappedReadFilter implements SamRecordFilter {
+public class UnmappedReadFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getReadUnmappedFlag() || read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
index 311d83cd0..7e6fc5e82 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
@@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
  * @version 0.1
  */
 
-public class ZeroMappingQualityReadFilter implements SamRecordFilter {
+public class ZeroMappingQualityReadFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (rec.getMappingQuality() == 0);
     }
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 62e0f257a..6119e20a6 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
@@ -169,7 +170,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
                 }
             }
 
-            for (Class<? extends SamRecordFilter> filter: filterManager.getValues()) {
+            for (Class<? extends ReadFilter> filter: filterManager.getValues()) {
                 String filterName = filterManager.getName(filter);
                 writeFilter(filterName, ArgumentDefinitionField.getArgumentFields(new ParsingEngine(null),filter), dependents);
             }
diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
index 7a03b76db..32d3675b7 100644
--- a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
@@ -5,6 +5,7 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.testng.Assert;
@@ -302,7 +303,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
                 null,
                 null,
                 new ValidationExclusion(),
-                new ArrayList<SamRecordFilter>(),
+                Collections.<ReadFilter>emptyList(),
                 false,
                 false,
                 BAQ.CalculationMode.OFF,