diff --git a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
index 86ca6c2df..f920d90ef 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
@@ -92,7 +92,10 @@ public final class IntervalBinding<T extends Feature> {
                 codec.readHeader(lineReader);
                 String line = lineReader.readLine();
                 while ( line != null ) {
-                    intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
+                    final Feature feature = codec.decodeLoc(line);
+                    if ( feature == null )
+                        throw new UserException.MalformedFile(featureIntervals.getSource(), "Couldn't parse line '" + line + "'");
+                    intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
                     line = lineReader.readLine();
                 }
             } catch (IOException e) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index 46d28185b..37a6cfc36 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -129,8 +129,14 @@ public class MalformedReadFilter extends ReadFilter {
      * @return true if they have the same number. False otherwise.
      */
     private static boolean checkMismatchingBasesAndQuals(SAMRecord read, boolean filterMismatchingBaseAndQuals) {
-        if (!filterMismatchingBaseAndQuals)
-            throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +"  [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
-        return (read.getReadLength() == read.getBaseQualities().length);
+        boolean result;
+        if (read.getReadLength() == read.getBaseQualities().length)
+            result = true;
+        else if (filterMismatchingBaseAndQuals)
+            result = false;
+        else
+            throw new UserException.MalformedBAM(read, String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals]", read.getReadName(), read.getReadLength(), read.getBaseQualities().length));
+
+        return result;
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 28f4f2a56..4e4a1550d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -15,11 +16,14 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.IntervalStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.JexlExpression;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
@@ -143,10 +147,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     /**
      * See the -list argument to view available modules.
      */
-    @Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)", required=false)
+    @Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)", required=false)
     protected String[] MODULES_TO_USE = {};
 
-    @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)", required=false)
+    @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -EV option)", required=false)
     protected Boolean NO_STANDARD_MODULES = false;
 
     // Other arguments
@@ -171,6 +175,19 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     @Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping", required=false)
     private boolean requireStrictAlleleMatch = false;
 
+    /**
+     * If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
+     * variant set, and evaluate the union of the results.  Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
+     */
+    @Argument(fullName="mergeEvals", shortName="mergeEvals", doc="If provided, all -eval tracks will be merged into a single eval track", required=false)
+    public boolean mergeEvals = false;
+
+    /**
+     * File containing tribble-readable features for the IntervalStratificiation
+     */
+    @Input(fullName="stratIntervals", shortName="stratIntervals", doc="File containing tribble-readable features for the IntervalStratificiation", required=false)
+    protected IntervalBinding<Feature> intervalsFile = null;
+
     // Variables
     private Set<SortableJexlVCMatchExp> jexlExpressions = new TreeSet<SortableJexlVCMatchExp>();
 
@@ -224,13 +241,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                 knowns.add(compRod);
         }
 
-        // Collect the eval rod names
-        Set<String> evalNames = new TreeSet<String>();
-        for ( RodBinding<VariantContext> evalRod : evals )
-            evalNames.add(evalRod.getName());
-
         // Now that we have all the rods categorized, determine the sample list from the eval rods.
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evalNames);
+        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evals);
         Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
 
         // Load the sample list
@@ -258,6 +270,16 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                 perSampleIsEnabled = true;
         }
 
+        if ( intervalsFile != null ) {
+            boolean fail = true;
+            for ( final VariantStratifier vs : stratificationObjects ) {
+                if ( vs.getClass().equals(IntervalStratification.class) )
+                    fail = false;
+            }
+            if ( fail )
+                throw new UserException.BadArgumentValue("ST", "stratIntervals argument provided but -ST IntervalStratification not provided");
+        }
+
         // Initialize the evaluation contexts
         evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);
 
@@ -289,8 +311,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
             String aastr = (ancestralAlignments == null) ? null : new String(ancestralAlignments.getSubsequenceAt(ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop()).getBases());
 
             //      --------- track ---------           sample  - VariantContexts -
-            HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled);
-            HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false);
+            HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
+            HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
 
             // for each eval track
             for ( final RodBinding<VariantContext> evalRod : evals ) {
@@ -353,6 +375,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                         }
                     }
                 }
+
+                if ( mergeEvals ) break; // stop processing the eval tracks
             }
         }
 
@@ -528,6 +552,14 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
     public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }
 
+    public List<GenomeLoc> getIntervals() {
+        if ( intervalsFile == null )
+            throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled");
+
+        return intervalsFile.getIntervals(getToolkit());
+    }
+
+
     public Set<String> getContigNames() {
         final TreeSet<String> contigs = new TreeSet<String>();
         for( final SAMSequenceRecord r :  getToolkit().getReferenceDataSource().getReference().getSequenceDictionary().getSequences()) {
@@ -536,4 +568,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
         return contigs;
     }
 
+    public GenomeLocParser getGenomeLocParser() {
+        return getToolkit().getGenomeLocParser();
+    }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index e83434037..cba2781d8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -41,6 +41,9 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     public long nDeletions = 0;
     @DataPoint(description = "Number of complex indels")
     public long nComplex = 0;
+    @DataPoint(description = "Number of symbolic events")
+    public long nSymbolic = 0;
+
     @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
     public long nMixed = 0;
 
@@ -131,8 +134,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nMixed++;
                     break;
                 case SYMBOLIC:
-                    // ignore symbolic alleles, but don't fail
-                    // todo - consistent way of treating symbolic alleles thgoughout codebase?
+                    nSymbolic++;
                     break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
new file mode 100644
index 000000000..3ab618496
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.EnumMap;
+import java.util.HashMap;
+import java.util.Map;
+
+@Analysis(description = "Build 1000 Genome Phase I paper summary of variants table")
+public class G1KPhaseITable extends VariantEvaluator {
+    // basic counts on various rates found
+    @DataPoint(description = "Number of samples")
+    public long nSamples = 0;
+
+    @DataPoint(description = "Number of processed loci")
+    public long nProcessedLoci = 0;
+
+    @DataPoint(description = "Number of SNPs")
+    public long nSNPs = 0;
+    @DataPoint(description = "SNP Novelty Rate")
+    public double SNPNoveltyRate = 0;
+    @DataPoint(description = "Mean number of SNPs per individual")
+    public long nSNPsPerSample = 0;
+
+    @DataPoint(description = "Number of Indels")
+    public long nIndels = 0;
+    @DataPoint(description = "Indel Novelty Rate")
+    public double IndelNoveltyRate = 0;
+    @DataPoint(description = "Mean number of Indels per individual")
+    public long nIndelsPerSample = 0;
+
+    @DataPoint(description = "Number of SVs")
+    public long nSVs = 0;
+    @DataPoint(description = "SV Novelty Rate")
+    public double SVNoveltyRate = 0;
+    @DataPoint(description = "Mean number of SVs per individual")
+    public long nSVsPerSample = 0;
+
+    Map<VariantContext.Type, Integer> allVariantCounts, knownVariantCounts;
+    Map<String, Map<VariantContext.Type, Integer>> countsPerSample;
+
+    private final Map<VariantContext.Type, Integer> makeCounts() {
+        Map<VariantContext.Type, Integer> counts = new EnumMap<VariantContext.Type, Integer>(VariantContext.Type.class);
+        counts.put(VariantContext.Type.SNP, 0);
+        counts.put(VariantContext.Type.INDEL, 0);
+        counts.put(VariantContext.Type.SYMBOLIC, 0);
+        return counts;
+    }
+
+    public void initialize(VariantEvalWalker walker) {
+        countsPerSample = new HashMap<String, Map<VariantContext.Type, Integer>>();
+        nSamples = walker.getSampleNamesForEvaluation().size();
+
+        for ( String sample : walker.getSampleNamesForEvaluation() ) {
+            countsPerSample.put(sample, makeCounts());
+        }
+
+        allVariantCounts = makeCounts();
+        knownVariantCounts = makeCounts();
+    }
+
+    @Override public boolean enabled() { return true; }
+
+    public int getComparisonOrder() {
+        return 2;   // we only need to see each eval track
+    }
+
+    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
+    }
+
+    public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( eval == null || eval.isMonomorphic() ) return null;
+
+        switch (eval.getType()) {
+//            case NO_VARIATION:
+//                // shouldn't get here
+//                break;
+            case SNP:
+            case INDEL:
+            case SYMBOLIC:
+                allVariantCounts.put(eval.getType(), allVariantCounts.get(eval.getType()) + 1);
+                if ( comp != null )
+                    knownVariantCounts.put(eval.getType(), knownVariantCounts.get(eval.getType()) + 1);
+                break;
+            default:
+                throw new UserException.BadInput("Unexpected variant context type: " + eval);
+        }
+
+        // count variants per sample
+        for (final Genotype g : eval.getGenotypes().values()) {
+            if ( ! g.isNoCall() && ! g.isHomRef() ) {
+                int count = countsPerSample.get(g.getSampleName()).get(eval.getType());
+                countsPerSample.get(g.getSampleName()).put(eval.getType(), count + 1);
+            }
+        }
+
+        return null; // we don't capture any interesting sites
+    }
+
+    private final int perSampleMean(VariantContext.Type type) {
+        long sum = 0;
+        for ( Map<VariantContext.Type, Integer> count : countsPerSample.values() ) {
+            sum += count.get(type);
+        }
+        return (int)(Math.round(sum / (1.0 * countsPerSample.size())));
+    }
+
+    private final double noveltyRate(VariantContext.Type type) {
+        int all = allVariantCounts.get(type);
+        int known = knownVariantCounts.get(type);
+        int novel = all - known;
+        return (novel / (1.0 * all));
+    }
+
+    public void finalizeEvaluation() {
+        nSNPs = allVariantCounts.get(VariantContext.Type.SNP);
+        nIndels = allVariantCounts.get(VariantContext.Type.INDEL);
+        nSVs = allVariantCounts.get(VariantContext.Type.SYMBOLIC);
+
+        nSNPsPerSample = perSampleMean(VariantContext.Type.SNP);
+        nIndelsPerSample = perSampleMean(VariantContext.Type.INDEL);
+        nSVsPerSample = perSampleMean(VariantContext.Type.SYMBOLIC);
+
+        SNPNoveltyRate = noveltyRate(VariantContext.Type.SNP);
+        IndelNoveltyRate = noveltyRate(VariantContext.Type.INDEL);
+        SVNoveltyRate = noveltyRate(VariantContext.Type.SYMBOLIC);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index e276adc32..b2b6d4165 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -15,8 +16,11 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
     @Override
     public void initialize() {
         states = new ArrayList<String>();
-        for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getEvals() )
+        for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getEvals() ) {
             states.add(rod.getName());
+            if ( getVariantEvalWalker().mergeEvals )
+                break;
+        }
     }
 
     public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
new file mode 100644
index 000000000..bf001588a
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
@@ -0,0 +1,93 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+
+import net.sf.picard.util.IntervalTree;
+import org.apache.log4j.Logger;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+
+/**
+ * Stratifies the variants by whether they overlap an interval in the set provided on the command line.
+ *
+ * The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up
+ * by whether a variant overlaps an interval or not.  I use this to differentiate between variants occurring
+ * in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
+ *
+ * -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
+ *
+ * Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value.  In order to
+ * safely use this module you should provide entire contigs worth of variants, and let the interval strat decide
+ * overlap, as opposed to using -L which will not properly work with symbolic variants.
+ */
+public class IntervalStratification extends VariantStratifier {
+    final protected static Logger logger = Logger.getLogger(IntervalStratification.class);
+    final Map<String, IntervalTree<Boolean>> intervalTreeByContig = new HashMap<String, IntervalTree<Boolean>>();
+
+    @Override
+    public void initialize() {
+        final List<GenomeLoc> locs = getVariantEvalWalker().getIntervals();
+
+        if ( locs.isEmpty() )
+            throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals.  Perhaps the file is malformed or empty?");
+
+        logger.info(String.format("Creating IntervalStratification containing %d intervals covering %d bp",
+                locs.size(), IntervalUtils.intervalSize(locs)));
+
+        // set up the map from contig -> interval tree
+        for ( final String contig : getVariantEvalWalker().getContigNames() )
+            intervalTreeByContig.put(contig, new IntervalTree<Boolean>());
+
+        for ( final GenomeLoc loc : locs ) {
+            intervalTreeByContig.get(loc.getContig()).put(loc.getStart(), loc.getStop(), true);
+        }
+
+        states = new ArrayList<String>(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
+    }
+
+    public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+        final ArrayList<String> relevantStates = new ArrayList<String>(Arrays.asList("all"));
+
+        if (eval != null) {
+            final GenomeLoc loc = getVariantEvalWalker().getGenomeLocParser().createGenomeLoc(eval, true);
+            IntervalTree<Boolean> intervalTree = intervalTreeByContig.get(loc.getContig());
+            IntervalTree.Node<Boolean> node = intervalTree.minOverlapper(loc.getStart(), loc.getStop());
+            //logger.info(String.format("Overlap %s found %s", loc, node));
+            relevantStates.add( node != null ? "overlaps.intervals" : "outside.intervals");
+        }
+
+        return relevantStates;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index 6a057a456..aa8c6cfb9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -312,12 +312,20 @@ public class VariantEvalUtils {
      *
      * @return the mapping of track to VC list that should be populated
      */
-    public HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, List<RodBinding<VariantContext>> tracks, boolean byFilter, boolean subsetBySample, boolean trackPerSample) {
+    public HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>
+        bindVariantContexts(RefMetaDataTracker tracker,
+                            ReferenceContext ref,
+                            List<RodBinding<VariantContext>> tracks,
+                            boolean byFilter,
+                            boolean subsetBySample,
+                            boolean trackPerSample,
+                            boolean mergeTracks) {
         if ( tracker == null )
             return null;
 
         HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> bindings = new HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>();
 
+        RodBinding<VariantContext> firstTrack = tracks.isEmpty() ? null : tracks.get(0);
         for ( RodBinding<VariantContext> track : tracks ) {
             HashMap<String, Set<VariantContext>> mapping = new HashMap<String, Set<VariantContext>>();
 
@@ -346,7 +354,20 @@ public class VariantEvalUtils {
                 }
             }
 
-            bindings.put(track, mapping);
+            if ( mergeTracks && bindings.containsKey(firstTrack) ) {
+                // go through each binding of sample -> value and add all of the bindings from this entry
+                HashMap<String, Set<VariantContext>> firstMapping = bindings.get(firstTrack);
+                for ( Map.Entry<String, Set<VariantContext>> elt : mapping.entrySet() ) {
+                    Set<VariantContext> firstMappingSet = firstMapping.get(elt.getKey());
+                    if ( firstMappingSet != null ) {
+                        firstMappingSet.addAll(elt.getValue());
+                    } else {
+                        firstMapping.put(elt.getKey(), elt.getValue());
+                    }
+                }
+            } else {
+                bindings.put(track, mapping);
+            }
         }
 
         return bindings;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index ce03dfffe..573e15971 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -162,7 +162,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     private boolean sitesOnlyVCF = false;
 
     public void initialize() {
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
+        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
 
         if ( PRIORITY_STRING == null ) {
             PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8d9768681..e10bcbaa0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -35,8 +35,10 @@ import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * Factory class for creating GenomeLocs
@@ -453,6 +455,28 @@ public class GenomeLocParser {
         return createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
     }
 
+    /**
+     * Creates a GenomeLoc corresponding to the variant context vc.  If includeSymbolicEndIfPossible
+     * is true, and VC is a symbolic allele the end of the created genome loc will be the value
+     * of the END info field key, if it exists, or vc.getEnd() if not.
+     *
+     * @param vc
+     * @param includeSymbolicEndIfPossible
+     * @return
+     */
+    public GenomeLoc createGenomeLoc(final VariantContext vc, boolean includeSymbolicEndIfPossible) {
+        if ( includeSymbolicEndIfPossible && vc.isSymbolic() ) {
+            int end = vc.getAttributeAsInt(VCFConstants.END_KEY, vc.getEnd());
+            return createGenomeLoc(vc.getChr(), vc.getStart(), end);
+        }
+        else
+            return createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd());
+    }
+
+    public GenomeLoc createGenomeLoc(final VariantContext vc) {
+        return createGenomeLoc(vc, false);
+    }
+
     /**
      * create a new genome loc, given the contig name, and a single position. Must be on the reference
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index edc1413ba..68b220aab 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -150,7 +150,7 @@ public class SampleUtils {
 
         // iterate to get all of the sample names
 
-        for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit, null).entrySet() ) {
+        for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
             Set<String> vcfSamples = pair.getValue().getGenotypeSamples();
             for ( String sample : vcfSamples )
                 addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey());
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index 2d8421507..5bd6a9b32 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -26,6 +26,8 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.apache.log4j.Logger;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -41,6 +43,18 @@ public class VCFUtils {
      */
     private VCFUtils() { }
 
+    public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
+        // Collect the eval rod names
+        final Set<String> names = new TreeSet<String>();
+        for ( final RodBinding<T> evalRod : rodBindings )
+            names.add(evalRod.getName());
+        return getVCFHeadersFromRods(toolkit, names);
+    }
+
+    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
+        return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
+    }
+
     public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
         Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index cbfe0ceab..3dceb9bd2 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -70,7 +70,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
+                                Arrays.asList("fb926edfd3d811e18b33798a43ef4379")
                               );
         executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
     }
@@ -91,7 +91,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("d470e00a368b5a0468012818994c6a89")
+                Arrays.asList("26b7d57e3a204ac80a28cb29485b59b7")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
     }
@@ -113,7 +113,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("12856e52c2682328f91594089328596c")
+                Arrays.asList("1df8184062f330bea9da8bacacc5a09d")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
     }
@@ -134,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
+                Arrays.asList("927f26414509db9e7c0a2c067d57c949")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
     }
@@ -155,7 +155,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
+                Arrays.asList("e6fddefd95122cabc5a0f0b95bce6d34")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
     }
@@ -176,7 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("15beaf3823c131cabc5fb0445239f978")
+                Arrays.asList("df10486dae73a9cf8c647964f51ba3e0")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
     }
@@ -197,7 +197,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
+                Arrays.asList("524adb0b7ff70e227b8803a88f36713e")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
     }
@@ -220,7 +220,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
+                Arrays.asList("ef6449789dfc032602458b7c5538a1bc")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
     }
@@ -245,7 +245,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
+                Arrays.asList("13b90e94fa82d72bb04a0a5addb27c3f")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
     }
@@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
+                Arrays.asList("8458b9d7803d75aae551fac7dbd152d6")
         );
         executeTest("testFundamentalsCountVariantsNoCompRod", spec);
     }
@@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
                 " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
-                1, Arrays.asList("f70997b6a3e7fdc89d11e1d61a2463d4"));
+                1, Arrays.asList("b954dee127ec4205ed7d33c91aa3e045"));
         executeTestParallel("testSelect1", spec);
     }
 
@@ -294,7 +294,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompVsEvalAC() {
         String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("407682de41dcf139ea635e9cda21b912"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ae0027197547731a9a5c1eec5fbe0221"));
         executeTestParallel("testCompVsEvalAC",spec);
     }
 
@@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            " --dbsnp " + b37dbSNP132 +
                            " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
                            " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("424c9d438b1faa59b2c29413ba32f37b"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("835b44fc3004cc975c968c9f92ed25d6"));
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
@@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
                 " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
                 " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18fa0b89ebfff51141975d7e4ce7a159"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("f0e003f1293343c3210ae95e8936b19a"));
         executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
     }
 
@@ -414,8 +414,29 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
+                                Arrays.asList("924b6123edb9da540d0abc66f6f33e16")
                               );
         executeTest("testAlleleCountStrat", spec);
     }
+
+    @Test
+    public void testIntervalStrat() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                                buildCommandLine(
+                                        "-T VariantEval",
+                                        "-R " + b37KGReference,
+                                        "-eval " + testDir + "/withSymbolic.b37.vcf",
+                                        "-noEV",
+                                        "-EV CountVariants",
+                                        "-noST",
+                                        "-stratIntervals " + testDir + "/overlapTest.bed",
+                                        "-ST IntervalStratification",
+                                        "-L 20",
+                                        "-o %s"
+                                ),
+                                1,
+                                Arrays.asList("9794e2dba205c6929dc89899fdf0bf6b")
+                              );
+        executeTest("testIntervalStrat", spec);
+    }
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index e8091cde7..768eab7e4 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -129,9 +129,11 @@ class QCommandLine extends CommandLineProgram with Logging {
           logger.info("Writing JobLogging GATKReport to file " + reportFile)
           QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), reportFile)
 
-          val pdfFile = new File(jobStringName + ".pdf")
-          logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
-          QJobReport.plotReport(reportFile, pdfFile)
+          if ( settings.run ) {
+            val pdfFile = new File(jobStringName + ".pdf")
+            logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
+            QJobReport.plotReport(reportFile, pdfFile)
+          }
         }
       }
     }
diff --git a/public/testdata/overlapTest.bed b/public/testdata/overlapTest.bed
new file mode 100644
index 000000000..6859f1fdc
--- /dev/null
+++ b/public/testdata/overlapTest.bed
@@ -0,0 +1,3 @@
+20 315000 315100 # should overlap 2 in withSymbolic.vcf at 315006 and 315072
+20 316955 316959 # should overlap only deletion variant at 316952
+20 317900 400000 # should overlap only the symbolic variant at 317173
diff --git a/public/testdata/withSymbolic.b37.vcf b/public/testdata/withSymbolic.b37.vcf
new file mode 100644
index 000000000..4974f1229
--- /dev/null
+++ b/public/testdata/withSymbolic.b37.vcf
@@ -0,0 +1,96 @@
+##fileformat=VCFv4.1
+##INFO=<ID=LCSNP,Number=0,Type=Flag,Description="Genotype likelihood in Low coverage VCF in data integration">
+##INFO=<ID=EXSNP,Number=0,Type=Flag,Description="Genotype likelihood in Exome VCF in data integration">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Genotype likelihood in INDEL VCF in data integration">
+##INFO=<ID=SV,Number=0,Type=Flag,Description="Genotype likelihood in SV VCF in data integration">
+##INFO=<ID=BAVGPOST,Number=1,Type=Float,Description="Average posterior probability from beagle">
+##INFO=<ID=BRSQ,Number=1,Type=Float,Description="Genotype imputation quality estimate from beagle">
+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SOURCE,Number=.,Type=String,Description="Source of deletion call">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
+##ALT=<ID=DEL,Description="Deletion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
+##FORMAT=<ID=BD,Number=1,Type=Float,Description="Genotype dosage from beagle">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	315006	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.721;LDAF=0.0025;AVGPOST=0.9978;RSQ=0.6449;ERATE=0.0008;THETA=0.0006;AC=4;AN=2184
+20	315072	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.996;LDAF=0.0057;AVGPOST=0.9996;RSQ=0.9743;ERATE=0.0003;THETA=0.0016;AC=12;AN=2184
+20	315162	.	T	G	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.950;LDAF=0.0005;AVGPOST=0.9998;RSQ=0.8078;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
+20	315168	rs71327439	G	GA	7142	PASS	INDEL;BAVGPOST=0.999;BRSQ=0.990;LDAF=0.0575;AVGPOST=0.9985;RSQ=0.9891;ERATE=0.0003;THETA=0.0004;AC=125;AN=2184
+20	315201	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.965;LDAF=0.0005;AVGPOST=0.9999;RSQ=0.8599;ERATE=0.0003;THETA=0.0008;AC=1;AN=2184
+20	315214	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.974;LDAF=0.0009;AVGPOST=0.9990;RSQ=0.5860;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
+20	315270	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0557;AVGPOST=0.9992;RSQ=0.9950;ERATE=0.0003;THETA=0.0004;AC=121;AN=2184
+20	315279	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0572;AVGPOST=0.9990;RSQ=0.9926;ERATE=0.0003;THETA=0.0013;AC=125;AN=2184
+20	315320	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.995;LDAF=0.0028;AVGPOST=0.9998;RSQ=0.9594;ERATE=0.0005;THETA=0.0003;AC=6;AN=2184
+20	315322	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.814;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6510;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
+20	315431	.	A	T	100	PASS	LCSNP;EXSNP;BAVGPOST=0.987;BRSQ=0.864;LDAF=0.0431;AVGPOST=0.9873;RSQ=0.8675;ERATE=0.0006;THETA=0.0010;AC=86;AN=2184
+20	315481	.	T	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0619;AVGPOST=0.9993;RSQ=0.9948;ERATE=0.0003;THETA=0.0007;AC=135;AN=2184
+20	315490	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.984;LDAF=0.0138;AVGPOST=0.9971;RSQ=0.9260;ERATE=0.0003;THETA=0.0046;AC=31;AN=2184
+20	315523	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.822;LDAF=0.0015;AVGPOST=0.9988;RSQ=0.6777;ERATE=0.0005;THETA=0.0003;AC=2;AN=2184
+20	315547	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.893;LDAF=0.0026;AVGPOST=0.9995;RSQ=0.9024;ERATE=0.0003;THETA=0.0004;AC=5;AN=2184
+20	315549	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.888;LDAF=0.0029;AVGPOST=0.9988;RSQ=0.8565;ERATE=0.0003;THETA=0.0013;AC=5;AN=2184
+20	315551	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.829;LDAF=0.0008;AVGPOST=0.9992;RSQ=0.5723;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
+20	315704	.	G	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.945;LDAF=0.0184;AVGPOST=0.9978;RSQ=0.9523;ERATE=0.0003;THETA=0.0017;AC=40;AN=2184
+20	315798	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.773;LDAF=0.0012;AVGPOST=0.9985;RSQ=0.4929;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
+20	315842	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.979;LDAF=0.0110;AVGPOST=0.9991;RSQ=0.9673;ERATE=0.0003;THETA=0.0005;AC=23;AN=2184
+20	315876	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.926;LDAF=0.0018;AVGPOST=0.9988;RSQ=0.7731;ERATE=0.0003;THETA=0.0007;AC=3;AN=2184
+20	316028	.	G	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0714;AVGPOST=0.9997;RSQ=0.9982;ERATE=0.0003;THETA=0.0003;AC=156;AN=2184
+20	316055	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.997;LDAF=0.1006;AVGPOST=0.9993;RSQ=0.9969;ERATE=0.0003;THETA=0.0007;AC=220;AN=2184
+20	316137	.	G	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.976;LDAF=0.0037;AVGPOST=0.9982;RSQ=0.7861;ERATE=0.0004;THETA=0.0009;AC=6;AN=2184
+20	316142	.	C	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.793;LDAF=0.0033;AVGPOST=0.9980;RSQ=0.7527;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
+20	316143	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.839;LDAF=0.0034;AVGPOST=0.9984;RSQ=0.8054;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
+20	316211	.	C	G	100	PASS	LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.976;LDAF=0.0565;AVGPOST=0.9983;RSQ=0.9872;ERATE=0.0003;THETA=0.0010;AC=124;AN=2184
+20	316285	.	A	AT	5514	PASS	INDEL;BAVGPOST=0.999;BRSQ=0.993;LDAF=0.0552;AVGPOST=0.9978;RSQ=0.9829;ERATE=0.0004;THETA=0.0005;AC=119;AN=2184
+20	316295	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.808;LDAF=0.0021;AVGPOST=0.9980;RSQ=0.6390;ERATE=0.0003;THETA=0.0008;AC=4;AN=2184
+20	316481	.	G	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0499;AVGPOST=0.9997;RSQ=0.9970;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
+20	316488	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.897;LDAF=0.0011;AVGPOST=0.9997;RSQ=0.8509;ERATE=0.0003;THETA=0.0006;AC=2;AN=2184
+20	316553	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.945;LDAF=0.0007;AVGPOST=0.9996;RSQ=0.7074;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
+20	316659	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0497;AVGPOST=0.9995;RSQ=0.9960;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
+20	316691	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.985;LDAF=0.0058;AVGPOST=0.9989;RSQ=0.9301;ERATE=0.0003;THETA=0.0003;AC=13;AN=2184
+20	316700	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.737;LDAF=0.0030;AVGPOST=0.9971;RSQ=0.5700;ERATE=0.0009;THETA=0.0016;AC=4;AN=2184
+20	316725	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.853;LDAF=0.0011;AVGPOST=0.9995;RSQ=0.7944;ERATE=0.0003;THETA=0.0004;AC=2;AN=2184
+20	316770	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.966;LDAF=0.0017;AVGPOST=0.9991;RSQ=0.7543;ERATE=0.0005;THETA=0.0005;AC=3;AN=2184
+20	316813	.	GTTC	G	1701	PASS	INDEL;BAVGPOST=0.995;BRSQ=0.850;LDAF=0.0156;AVGPOST=0.9987;RSQ=0.9611;ERATE=0.0003;THETA=0.0006;AC=34;AN=2184
+20	316824	rs11472305	T	TTTC	5129	PASS	INDEL;BAVGPOST=0.979;BRSQ=0.863;LDAF=0.0697;AVGPOST=0.9782;RSQ=0.8837;ERATE=0.0016;THETA=0.0006;AC=153;AN=2184
+20	316839	.	CT	C	1122	PASS	INDEL;BAVGPOST=0.980;BRSQ=0.804;LDAF=0.0505;AVGPOST=0.9743;RSQ=0.8100;ERATE=0.0040;THETA=0.0009;AC=104;AN=2184
+20	316841	.	TTC	T	1096	PASS	INDEL;BAVGPOST=0.981;BRSQ=0.824;LDAF=0.0491;AVGPOST=0.9783;RSQ=0.8367;ERATE=0.0029;THETA=0.0005;AC=105;AN=2184
+20	316842	.	TCC	T	110	PASS	INDEL;BAVGPOST=0.983;BRSQ=0.592;LDAF=0.0203;AVGPOST=0.9772;RSQ=0.5576;ERATE=0.0022;THETA=0.0005;AC=30;AN=2184
+20	316845	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.645;LDAF=0.0015;AVGPOST=0.9989;RSQ=0.6666;ERATE=0.0003;THETA=0.0010;AC=2;AN=2184
+20	316853	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.990;BRSQ=0.922;LDAF=0.0688;AVGPOST=0.9742;RSQ=0.8456;ERATE=0.0049;THETA=0.0006;AC=133;AN=2184
+20	316882	rs11479165	CT	C	145	PASS	INDEL;BAVGPOST=0.991;BRSQ=0.484;LDAF=0.0074;AVGPOST=0.9920;RSQ=0.5655;ERATE=0.0005;THETA=0.0014;AC=9;AN=2184
+20	316889	.	T	TTC	108	PASS	INDEL;BAVGPOST=0.978;BRSQ=0.235;LDAF=0.0521;AVGPOST=0.9304;RSQ=0.4479;ERATE=0.0035;THETA=0.0016;AC=63;AN=2184
+20	316901	.	T	TTC	272	PASS	INDEL;BAVGPOST=0.979;BRSQ=0.510;LDAF=0.0363;AVGPOST=0.9527;RSQ=0.4348;ERATE=0.0071;THETA=0.0003;AC=34;AN=2184
+20	316917	.	CT	C	67	PASS	INDEL;BAVGPOST=0.983;BRSQ=0.483;LDAF=0.0265;AVGPOST=0.9828;RSQ=0.7509;ERATE=0.0006;THETA=0.0011;AC=51;AN=2184
+20	316918	rs112071142	TTTC	T	3049	PASS	INDEL;BAVGPOST=0.980;BRSQ=0.801;LDAF=0.0588;AVGPOST=0.9761;RSQ=0.8444;ERATE=0.0026;THETA=0.0005;AC=120;AN=2184
+20	316924	.	CT	C	8	PASS	INDEL;BAVGPOST=0.999;BRSQ=0.581;LDAF=0.0053;AVGPOST=0.9932;RSQ=0.5513;ERATE=0.0004;THETA=0.0011;AC=6;AN=2184
+20	316936	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.994;BRSQ=0.651;LDAF=0.0098;AVGPOST=0.9884;RSQ=0.5505;ERATE=0.0018;THETA=0.0005;AC=13;AN=2184
+20	316939	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.720;LDAF=0.0071;AVGPOST=0.9899;RSQ=0.4845;ERATE=0.0010;THETA=0.0033;AC=8;AN=2184
+20	316952	.	CTCTTCCTCTTCT	C	15835	PASS	INDEL;BAVGPOST=0.891;BRSQ=0.667;LDAF=0.1650;AVGPOST=0.9042;RSQ=0.7274;ERATE=0.0037;THETA=0.0008;AC=294;AN=2184
+20	317003	.	TCC	T	333	PASS	INDEL;BAVGPOST=0.890;BRSQ=0.114;LDAF=0.3450;AVGPOST=0.5526;RSQ=0.1674;ERATE=0.0300;THETA=0.0011;AC=350;AN=2184
+20	317022	rs111424933	TTTC	T	4776	PASS	INDEL;BAVGPOST=0.982;BRSQ=0.865;LDAF=0.0561;AVGPOST=0.9837;RSQ=0.8889;ERATE=0.0017;THETA=0.0004;AC=110;AN=2184
+20	317057	.	C	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.775;LDAF=0.0014;AVGPOST=0.9985;RSQ=0.6049;ERATE=0.0003;THETA=0.0002;AC=3;AN=2184
+20	317135	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.992;LDAF=0.0489;AVGPOST=0.9964;RSQ=0.9749;ERATE=0.0004;THETA=0.0025;AC=106;AN=2184
+20	317173	MERGED_DEL_2_99440	A	<DEL>	.	.	SV;BAVGPOST=0.998;BRSQ=0.577;LDAF=0.0018;AVGPOST=0.9990;RSQ=0.7465;ERATE=0.0003;THETA=0.0007;CIEND=-61,92;CIPOS=-84,73;END=319201;SOURCE=BreakDancer_317182_319211,GenomeStrip_317164_319190;SVTYPE=DEL;AC=2;AN=2184
+20	317174	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.991;LDAF=0.0502;AVGPOST=0.9962;RSQ=0.9727;ERATE=0.0005;THETA=0.0007;AC=107;AN=2184
+20	317266	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.999;LDAF=0.1748;AVGPOST=0.9988;RSQ=0.9973;ERATE=0.0003;THETA=0.0005;AC=383;AN=2184
+20	317448	.	A	G	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0068;AVGPOST=0.9988;RSQ=0.9405;ERATE=0.0003;THETA=0.0002;AC=16;AN=2184
+20	317491	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0609;AVGPOST=0.9993;RSQ=0.9939;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
+20	317546	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.837;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6154;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
+20	317578	.	C	T	100	PASS	LCSNP;EXSNP;BAVGPOST=0.996;BRSQ=0.882;LDAF=0.0180;AVGPOST=0.9981;RSQ=0.9606;ERATE=0.0003;THETA=0.0004;AC=40;AN=2184
+20	317658	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0609;AVGPOST=0.9998;RSQ=0.9980;ERATE=0.0003;THETA=0.0005;AC=133;AN=2184
+20	317676	.	T	C	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0608;AVGPOST=0.9999;RSQ=0.9992;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
+20	317710	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.952;LDAF=0.0014;AVGPOST=0.9997;RSQ=0.8880;ERATE=0.0004;THETA=0.0008;AC=3;AN=2184
+20	317824	.	G	A	100	PASS	LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0555;AVGPOST=0.9993;RSQ=0.9947;ERATE=0.0003;THETA=0.0009;AC=121;AN=2184