diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index 21971e189..52ac783a9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -105,11 +105,10 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
         ActiveRegionExtension annotation = walker.getClass().getAnnotation(ActiveRegionExtension.class);
         this.activeRegionExtension = this.walker.activeRegionExtension == null ? annotation.extension() : this.walker.activeRegionExtension;
         this.maxRegionSize = this.walker.activeRegionMaxSize == null ? annotation.maxRegion() : this.walker.activeRegionMaxSize;
-        final int bandPassFilterSize = this.walker.bandPassFilterSize == null ? annotation.bandPassFilterSize() : this.walker.bandPassFilterSize;
         final double bandPassSigma = this.walker.bandPassSigma == null ? annotation.bandPassSigma() : this.walker.bandPassSigma;
         walkerHasPresetRegions = this.walker.hasPresetActiveRegions();
 
-        activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), bandPassFilterSize, bandPassSigma);
+        activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma);
         if ( walkerHasPresetRegions ) {
             // we load all of the preset locations into the
             for ( final GenomeLoc loc : this.walker.getPresetActiveRegions()) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java
index 07723bfe2..72c409f62 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java
@@ -45,14 +45,6 @@ public @interface ActiveRegionExtension {
     public int extension() default 0;
     public int maxRegion() default 1500;
 
-    /**
-     * The size of the band pass filter in bp.  The filter size describes how far
-     * from the current site the band pass extends.  So a value of 1 implies a total
-     * band size of 3 bp, the site bp and one on each side
-     * @return
-     */
-    public int bandPassFilterSize() default BandPassActivityProfile.DEFAULT_FILTER_SIZE;
-
     /**
      * The sigma value for the Gaussian kernel of the band pass filter
      * @return
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index d2c92b6c3..92504e3ba 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -92,10 +92,6 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     @Argument(fullName="activeRegionMaxSize", shortName="activeRegionMaxSize", doc="The active region maximum size; if not provided defaults to Walker annotated default", required = false)
     public Integer activeRegionMaxSize = null;
 
-    @Advanced
-    @Argument(fullName="bandPassFilterSize", shortName="bandPassFilterSize", doc="The filter size of band pass filter; if not provided defaults to Walker annotated default", required = false)
-    public Integer bandPassFilterSize = null;
-
     @Advanced
     @Argument(fullName="bandPassSigma", shortName="bandPassSigma", doc="The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default", required = false)
     public Double bandPassSigma = null;
diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java
index 5c6389c26..75ae72f9e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java
@@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.LinkedList;
 
@@ -43,42 +44,55 @@ import java.util.LinkedList;
  * @since 2011
  */
 public class BandPassActivityProfile extends ActivityProfile {
-    public static final int DEFAULT_FILTER_SIZE = 80;
-    public static final double DEFAULT_SIGMA = 55.0;
+    public static final int MAX_FILTER_SIZE = 50;
+    private final static double MIN_PROB_TO_KEEP_IN_FILTER = 1e-5;
+    public static final double DEFAULT_SIGMA = 17.0;
 
     private final int filterSize;
     private final double sigma;
     private final double[] GaussianKernel;
 
-    /**
-     * Create a band pass activity profile with the default band size
-     * @param parser our genome loc parser
-     */
-    public BandPassActivityProfile(final GenomeLocParser parser) {
-        this(parser, DEFAULT_FILTER_SIZE, DEFAULT_SIGMA);
-    }
-
     /**
      * Create an activity profile that implements a band pass filter on the states
      * @param parser our genome loc parser
-     * @param filterSize the size (in bp) of the band pass filter.  The filter size is the number of bp to each
-     *                   side that are included in the band.  So a filter size of 1 implies that the actual band
-     *                   is 3 bp, 1 for the center site and 1 on each size.  2 => 5, etc.
+     * @param maxFilterSize the maximum size of the band pass filter we are allowed to create, regardless of sigma
+     * @param sigma the variance of the Gaussian kernel for this band pass filter
      */
-    public BandPassActivityProfile(final GenomeLocParser parser, final int filterSize, final double sigma) {
+    public BandPassActivityProfile(final GenomeLocParser parser, final int maxFilterSize, final double sigma) {
+        this(parser, maxFilterSize, sigma, true);
+    }
+
+    public BandPassActivityProfile(final GenomeLocParser parser, final int maxFilterSize, final double sigma, final boolean adaptiveFilterSize) {
         super(parser);
 
-        if ( filterSize < 0 ) throw new IllegalArgumentException("Filter size must be greater than or equal to 0 but got " + filterSize);
         if ( sigma < 0 ) throw new IllegalArgumentException("Sigma must be greater than or equal to 0 but got " + sigma);
 
         // setup the Gaussian kernel for the band pass filter
-        this.filterSize = filterSize;
         this.sigma = sigma;
-        final double[] kernel = new double[getBandSize()];
-        for( int iii = 0; iii < 2* filterSize + 1; iii++ ) {
+        final double[] fullKernel = makeKernel(maxFilterSize, sigma);
+        this.filterSize = adaptiveFilterSize ? determineFilterSize(fullKernel, MIN_PROB_TO_KEEP_IN_FILTER) : maxFilterSize;
+        this.GaussianKernel = makeKernel(this.filterSize, sigma);
+    }
+
+    protected static int determineFilterSize(final double[] kernel, final double minProbToKeepInFilter) {
+        final int middle = (kernel.length - 1) / 2;
+        int filterEnd = middle;
+        while ( filterEnd > 0 ) {
+            if ( kernel[filterEnd - 1] < minProbToKeepInFilter ) {
+                break;
+            }
+            filterEnd--;
+        }
+        return middle - filterEnd;
+    }
+
+    protected static double[] makeKernel(final int filterSize, final double sigma) {
+        final int bandSize = 2 * filterSize + 1;
+        final double[] kernel = new double[bandSize];
+        for( int iii = 0; iii < bandSize; iii++ ) {
             kernel[iii] = MathUtils.NormalDistribution(filterSize, sigma, iii);
         }
-        this.GaussianKernel = MathUtils.normalizeFromRealSpace(kernel);
+        return MathUtils.normalizeFromRealSpace(kernel);
     }
 
     /**
diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java
index 311d43206..bce1722cd 100644
--- a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java
@@ -87,7 +87,7 @@ public class ActivityProfileUnitTest extends BaseTest {
                 case Base: return new ActivityProfile(genomeLocParser);
                 case BandPass:
                     // zero size => equivalent to ActivityProfile
-                    return new BandPassActivityProfile(genomeLocParser, 0);
+                    return new BandPassActivityProfile(genomeLocParser, 0, 0.01, false);
                 default: throw new IllegalStateException(type.toString());
             }
         }
@@ -98,7 +98,7 @@ public class ActivityProfileUnitTest extends BaseTest {
                 int start = regionStart.getStart() + startsAndStops[i];
                 int end = regionStart.getStart() + startsAndStops[i+1] - 1;
                 GenomeLoc activeLoc = genomeLocParser.createGenomeLoc(regionStart.getContig(), start, end);
-                ActiveRegion r = new ActiveRegion(activeLoc, null, isActive, genomeLocParser, extension);
+                ActiveRegion r = new ActiveRegion(activeLoc, Collections.<ActivityProfileState>emptyList(), isActive, genomeLocParser, extension);
                 l.add(r);
                 isActive = ! isActive;
             }
diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
index 0a71bad14..ff1c9bdef 100644
--- a/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
@@ -81,7 +81,7 @@ public class BandPassActivityProfileUnitTest extends BaseTest {
 
     @Test(dataProvider = "BandPassBasicTest")
     public void testBandPass(final int start, final boolean precedingIsActive, final int nPrecedingSites, final int bandPassSize, final double sigma) {
-        final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize, sigma);
+        final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize, sigma, false);
 
         final int expectedBandSize = bandPassSize * 2 + 1;
         Assert.assertEquals(profile.getFilteredSize(), bandPassSize, "Wrong filter size");
@@ -124,7 +124,7 @@ public class BandPassActivityProfileUnitTest extends BaseTest {
     public Object[][] makeBandPassComposition() {
         final List<Object[]> tests = new LinkedList<Object[]>();
 
-        for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassActivityProfile.DEFAULT_FILTER_SIZE) ) {
+        for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassActivityProfile.MAX_FILTER_SIZE) ) {
             for ( int integrationLength : Arrays.asList(1, 10, 100, 1000) ) {
                 tests.add(new Object[]{ bandPassSize, integrationLength });
             }
@@ -167,4 +167,53 @@ public class BandPassActivityProfileUnitTest extends BaseTest {
             Assert.assertEquals(profile.getStateList().get(j).isActiveProb, expectedProbs[j], "State probability not expected at " + j);
         }
     }
+
+    // ------------------------------------------------------------------------------------
+    //
+    // Code to test the creation of the kernels
+    //
+    // ------------------------------------------------------------------------------------
+
+    /**
+
+     kernel <- function(sd, pThres) {
+     raw = dnorm(-80:81, mean=0, sd=sd)
+     norm = raw / sum(raw)
+     bad = norm < pThres
+     paste(norm[! bad], collapse=", ")
+     }
+
+     print(kernel(0.01, 1e-5))
+     print(kernel(1, 1e-5))
+     print(kernel(5, 1e-5))
+     print(kernel(17, 1e-5))
+
+     * @return
+     */
+
+    @DataProvider(name = "KernelCreation")
+    public Object[][] makeKernelCreation() {
+        final List<Object[]> tests = new LinkedList<Object[]>();
+
+        tests.add(new Object[]{ 0.01, 1000, new double[]{1.0}});
+        tests.add(new Object[]{ 1.0, 1000, new double[]{0.0001338302, 0.004431848, 0.053990966, 0.241970723, 0.398942278, 0.241970723, 0.053990966, 0.004431848, 0.0001338302}});
+        tests.add(new Object[]{ 1.0, 0, new double[]{1.0}});
+        tests.add(new Object[]{ 1.0, 1, new double[]{0.2740686, 0.4518628, 0.2740686}});
+        tests.add(new Object[]{ 1.0, 2, new double[]{0.05448868, 0.24420134, 0.40261995, 0.24420134, 0.05448868}});
+        tests.add(new Object[]{ 1.0, 1000, new double[]{0.0001338302, 0.004431848, 0.053990966, 0.241970723, 0.398942278, 0.241970723, 0.053990966, 0.004431848, 0.0001338302}});
+        tests.add(new Object[]{ 5.0, 1000, new double[]{1.1788613551308e-05, 2.67660451529771e-05, 5.83893851582921e-05, 0.000122380386022754, 0.000246443833694604, 0.000476817640292968, 0.000886369682387602, 0.00158309031659599, 0.00271659384673712, 0.00447890605896858, 0.00709491856924629, 0.0107981933026376, 0.0157900316601788, 0.0221841669358911, 0.029945493127149, 0.0388372109966426, 0.0483941449038287, 0.0579383105522965, 0.0666449205783599, 0.0736540280606647, 0.0782085387950912, 0.0797884560802865, 0.0782085387950912, 0.0736540280606647, 0.0666449205783599, 0.0579383105522965, 0.0483941449038287, 0.0388372109966426, 0.029945493127149, 0.0221841669358911, 0.0157900316601788, 0.0107981933026376, 0.00709491856924629, 0.00447890605896858, 0.00271659384673712, 0.00158309031659599, 0.000886369682387602, 0.000476817640292968, 0.000246443833694604, 0.000122380386022754, 5.83893851582921e-05, 2.67660451529771e-05, 1.1788613551308e-05}});
+        tests.add(new Object[]{17.0, 1000, new double[]{1.25162575710745e-05, 1.57001772728555e-05, 1.96260034693739e-05, 2.44487374842009e-05, 3.03513668801384e-05, 3.75489089511911e-05, 4.62928204154855e-05, 5.68757597480354e-05, 6.96366758708924e-05, 8.49661819944029e-05, 0.000103312156275406, 0.000125185491708561, 0.000151165896477646, 0.000181907623161359, 0.000218144981137171, 0.000260697461819069, 0.000310474281706066, 0.000368478124457557, 0.000435807841336874, 0.00051365985048857, 0.000603327960854364, 0.000706201337376934, 0.000823760321812988, 0.000957569829285965, 0.00110927005589186, 0.00128056425833231, 0.00147320340358764, 0.00168896753568649, 0.00192964376796036, 0.00219700088266432, 0.00249276060490197, 0.00281856571330067, 0.00317594525418154, 0.00356627723683793, 0.00399074930220799, 0.00445031797242299, 0.00494566720070898, 0.00547716704583487, 0.00604483338842317, 0.00664828968356621, 0.00728673180099395, 0.00795889703644795, 0.00866303838230695, 0.00939690511889675, 0.0101577307281371, 0.010942229037054, 0.0117465993701676, 0.0125665413280325, 0.0133972796167302, 0.0142335991336574, 0.0150698902735454, 0.0159002041614507, 0.0167183172536454, 0.0175178044808441, 0.0182921198494897, 0.0190346831745763, 0.0197389714002676, 0.020398612780527, 0.0210074820484496, 0.0215597946062309, 0.0220501977225941, 0.022473856734247, 0.0228265343139947, 0.0231046609899767, 0.0233053952756892, 0.0234266719946158, 0.0234672376502799, 0.0234266719946158, 0.0233053952756892, 0.0231046609899767, 0.0228265343139947, 0.022473856734247, 0.0220501977225941, 0.0215597946062309, 0.0210074820484496, 0.020398612780527, 0.0197389714002676, 0.0190346831745763, 0.0182921198494897, 0.0175178044808441, 0.0167183172536454, 0.0159002041614507, 0.0150698902735454, 0.0142335991336574, 0.0133972796167302, 0.0125665413280325, 0.0117465993701676, 0.010942229037054, 0.0101577307281371, 0.00939690511889675, 0.00866303838230695, 0.00795889703644795, 0.00728673180099395, 0.00664828968356621, 0.00604483338842317, 0.00547716704583487, 0.00494566720070898, 0.00445031797242299, 0.00399074930220799, 0.00356627723683793, 0.00317594525418154, 0.00281856571330067, 0.00249276060490197, 0.00219700088266432, 0.00192964376796036, 0.00168896753568649, 0.00147320340358764, 0.00128056425833231, 0.00110927005589186, 0.000957569829285965, 0.000823760321812988, 0.000706201337376934, 0.000603327960854364, 0.00051365985048857, 0.000435807841336874, 0.000368478124457557, 0.000310474281706066, 0.000260697461819069, 0.000218144981137171, 0.000181907623161359, 0.000151165896477646, 0.000125185491708561, 0.000103312156275406, 8.49661819944029e-05, 6.96366758708924e-05, 5.68757597480354e-05, 4.62928204154855e-05, 3.75489089511911e-05, 3.03513668801384e-05, 2.44487374842009e-05, 1.96260034693739e-05, 1.57001772728555e-05, 1.25162575710745e-05}});
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test( dataProvider = "KernelCreation")
+    public void testKernelCreation(final double sigma, final int maxSize, final double[] expectedKernel) {
+        final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, maxSize, sigma, true);
+
+        final double[] kernel = profile.getKernel();
+        Assert.assertEquals(kernel.length, expectedKernel.length);
+        for ( int i = 0; i < kernel.length; i++ )
+            Assert.assertEquals(kernel[i], expectedKernel[i], 1e-3, "Kernels not equal at " + i);
+    }
 }