Merge pull request #1187 from broadinstitute/ldg_variantEval_famStrat

Enable family-level stratification (if a ped file is provided)

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -350,6 +350,17 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec);
     }
 
+    @Test
+    public void testMVEvalFamilyStrat() {
+        String vcfFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf";
+        String pedFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped";
+
+        WalkerTestSpec spec = new WalkerTestSpec("-R "+b37KGReference+ " -T VariantEval -ped " + privateTestDir + pedFile + " -eval " + privateTestDir + vcfFile + " -noEV -noST -ST Family -EV MendelianViolationEvaluator -o %s",
+                1,
+                Arrays.asList("d599d3e6b308ac06b2c2e003cf596328"));
+        executeTestParallel("testMVEvalFamilyStrat", spec);
+    }
+
 
     private static String withSelect(String cmd, String select, String name) {
         return String.format("%s -select '%s' -selectName %s", cmd, select, name);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java

@@ -140,7 +140,7 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
         }
 
         @Override
-        public List<Object> getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName) {
+        public List<Object> getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName, final String familyName) {
             int i = Integer.valueOf(evalName); // a terrible hack, but we can now provide accessible states
             List<Object> states = new ArrayList<Object>();
             for ( int state : integers )
@@ -180,12 +180,12 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
         final RefMetaDataTracker tracker = new RefMetaDataTracker();
         final ReferenceContext ref = null;
         final VariantContext comp = null;
-        final String compName = null, sampleName = null;
+        final String compName = null, sampleName = null, familyName = null;
 
         // increment eval counts for each stratification of divisors of i from from 1...maxI
         for ( int i = 1; i <= cfg.maxI; i++ ) {
             final String evalName = String.valueOf(i); // terrible hack to stratify by divisor
-            for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName) ) {
+            for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName, familyName) ) {
                 synchronized (nec) {
                     nec.apply(tracker, ref, null, comp, eval);
                 }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java

@@ -29,8 +29,10 @@ import com.google.java.contract.Requires;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.util.IntervalTree;
 import htsjdk.samtools.SAMSequenceRecord;
+import oracle.jrockit.jfr.StringConstantPool;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
+import org.broadinstitute.gatk.engine.samples.Trio;
 import org.broadinstitute.gatk.engine.walkers.*;
 import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.*;
 import org.broadinstitute.gatk.utils.commandline.*;
@@ -105,7 +107,7 @@ import java.util.*;
  * </pre>
  * </p>
  *
- * <h3>Usage example</h3>
+ * <h3>Usage examples</h3>
  * <pre>
  * java -jar GenomeAnalysisTK.jar \
  *   -T VariantEval \
@@ -116,6 +118,18 @@ import java.util.*;
  *   [--comp comp.vcf]
  * </pre>
  *
+ * Count Mendelian violations for each family in a callset with multiple families (and provided pedigree)
+ * <pre>
+ * Java -jar GenomeAnalysisTK.jar \
+ *   -T VariantEval \
+ *   -R reference.fasta \
+ *   -o output.MVs.byFamily.table \
+ *   --eval multiFamilyCallset.vcf \
+ *   -noEV -noST \
+ *   -ST Family \
+ *   -EV MendelianViolationEvaluator
+ * </pre>
+ *
  * <h3>Caveat</h3>
  *
  * <p>Some stratifications and evaluators are incompatible with each other due to their respective memory requirements,
@@ -249,14 +263,18 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
 
     private boolean isSubsettingSamples;
     private Set<String> sampleNamesForEvaluation = new LinkedHashSet<String>();
+    private Set<String> familyNamesForEvaluation = new LinkedHashSet<String>();
     private Set<String> sampleNamesForStratification = new LinkedHashSet<String>();
+    private Set<String> familyNamesForStratification = new LinkedHashSet<String>();
 
     // important stratifications
     private boolean byFilterIsEnabled = false;
     private boolean perSampleIsEnabled = false;
+    private boolean perFamilyIsEnabled = false;
 
     // Public constants
-    private static String ALL_SAMPLE_NAME = "all";
+    final private static String ALL_SAMPLE_NAME = "all";
+    final private static String ALL_FAMILY_NAME = "all";
 
     // the number of processed bp for this walker
     long nProcessedLoci = 0;
@@ -303,12 +321,22 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
         final Set<String> allSampleNames = SampleUtils.getSamplesFromCommandLineInput(vcfSamples);
         sampleNamesForEvaluation.addAll(new TreeSet<String>(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS)));
         isSubsettingSamples = ! sampleNamesForEvaluation.containsAll(allSampleNames);
+        familyNamesForEvaluation.addAll(getSampleDB().getFamilyIDs());
 
-        if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
+        //If stratifying by sample name, assign a stratification for each sample we're evaluating (based on commandline args)...
+        if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample") ) {
             sampleNamesForStratification.addAll(sampleNamesForEvaluation);
         }
+        //...and also a stratification for the sum over all samples
         sampleNamesForStratification.add(ALL_SAMPLE_NAME);
 
+        //If stratifying by sample name, assign a stratification for each family...
+        if ( Arrays.asList(STRATIFICATIONS_TO_USE).contains("Family") ) {
+            familyNamesForStratification.addAll(familyNamesForEvaluation);
+        }
+        //...and also a stratification for the sum over all families
+        familyNamesForStratification.add(ALL_FAMILY_NAME);
+
         // Initialize select expressions
         for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
             SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
@@ -327,8 +355,17 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
                 byFilterIsEnabled = true;
             else if ( vs.getName().equals("Sample") )
                 perSampleIsEnabled = true;
+            else if ( vs.getName().equals("Family"))
+                perFamilyIsEnabled = true;
         }
 
+        if (perSampleIsEnabled && perFamilyIsEnabled)
+            throw new UserException.BadArgumentValue("ST", "Variants cannot be stratified by sample and family at the same time");
+
+        if (perFamilyIsEnabled && getSampleDB().getTrios().isEmpty())
+            throw new UserException.BadArgumentValue("ST", "Cannot stratify by family without *.ped file");
+
+
         if ( intervalsFile != null ) {
             boolean fail = true;
             for ( final VariantStratifier vs : stratificationObjects ) {
@@ -420,17 +457,24 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
 //            }
 
             //      --------- track ---------           sample  - VariantContexts -
-            HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
+            HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, perFamilyIsEnabled, mergeEvals);
-            HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
+            HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false, false);
 
             // for each eval track
             for ( final RodBinding<VariantContext> evalRod : evals ) {
                 final Map<String, Collection<VariantContext>> emptyEvalMap = Collections.emptyMap();
                 final Map<String, Collection<VariantContext>> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
 
+                Set<String> statificationLevels;
+
                 // for each sample stratifier
-                for ( final String sampleName : sampleNamesForStratification ) {
+                if (perFamilyIsEnabled)
-                    Collection<VariantContext> evalSetBySample = evalSet.get(sampleName);
+                    statificationLevels = familyNamesForStratification;
+                else
+                    statificationLevels = sampleNamesForStratification;
+                for ( final String stratLevelName : statificationLevels ) {
+                    Collection<VariantContext> evalSetBySample = evalSet.get(stratLevelName);
+
                     if ( evalSetBySample == null ) {
                         evalSetBySample = new HashSet<VariantContext>(1);
                         evalSetBySample.add(null);
@@ -452,7 +496,18 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
                             // find the comp
                             final VariantContext comp = findMatchingComp(eval, compSet);
 
-                            for ( EvaluationContext nec : getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), sampleName) ) {
+                            Collection<EvaluationContext> contextsForStratification;
+                            if (perFamilyIsEnabled)
+                                contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), null, stratLevelName);
+                            else {
+                                String familyID;
+                                if (stratLevelName.equals("all"))
+                                    familyID = "all";
+                                else
+                                    familyID = getSampleDB().getSample(stratLevelName).getFamilyID();
+                                contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), stratLevelName, familyID);
+                            }
+                            for ( EvaluationContext nec : contextsForStratification ) {
 
                                 // eval against the comp
                                 synchronized (nec) {
@@ -521,10 +576,11 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
                                                                   final String evalName,
                                                                   final VariantContext comp,
                                                                   final String compName,
-                                                                  final String sampleName ) {
+                                                                  final String sampleName,
+                                                                  final String familyName) {
         final List<List<Object>> states = new LinkedList<List<Object>>();
         for ( final VariantStratifier vs : stratManager.getStratifiers() ) {
-            states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName));
+            states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName, familyName));
         }
         return stratManager.values(states);
     }
@@ -649,6 +705,7 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
 
     public static String getAllSampleName() { return ALL_SAMPLE_NAME; }
+    public static String getAllFamilyName() { return ALL_FAMILY_NAME; }
 
     public List<RodBinding<VariantContext>> getKnowns() { return knowns; }
 
@@ -657,6 +714,8 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
     public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
 
+    public Set<String> getFamilyNamesForEvaluation() { return familyNamesForEvaluation; }
+
     public int getNumberOfSamplesForEvaluation() {
         if (sampleNamesForEvaluation!= null &&  !sampleNamesForEvaluation.isEmpty())
             return sampleNamesForEvaluation.size();
@@ -667,6 +726,8 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     }
     public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
 
+    public Set<String> getFamilyNamesForStratification() { return familyNamesForStratification; }
+
     public List<RodBinding<VariantContext>> getComps() { return comps; }
 
     public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java

@@ -172,7 +172,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
             HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef();
             HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar();
 
-            if(mv.getFamilyCalledCount()>0){
+            if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyCalledCount()>0){
                 nVariants++;
                 nFamCalled += mv.getFamilyCalledCount();
                 nLowQual += mv.getFamilyLowQualsCount();

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java

@@ -67,7 +67,7 @@ public class AlleleCount extends VariantStratifier {
         getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes");
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
         if (eval != null) {
             int AC = 0; // by default, the site is considered monomorphic
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java

@@ -47,7 +47,7 @@ public class AlleleFrequency extends VariantStratifier {
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             try {
                 return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3))));

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java

@@ -45,7 +45,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Collections.singletonList((Object)compName);
     }
 }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java

@@ -44,7 +44,7 @@ public class Contig extends VariantStratifier {
     }
 
     @Override
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             return Arrays.asList((Object)"all", eval.getChr());
         } else {

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java

@@ -53,7 +53,7 @@ public class CpG extends VariantStratifier {
     }
 
     @Override
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         boolean isCpG = false;
         if (ref != null && ref.getBases() != null) {
             String fwRefBases = new String(ref.getBases());

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java

@@ -103,7 +103,7 @@ public class Degeneracy extends VariantStratifier {
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList<Object> relevantStates = new ArrayList<Object>();
 
         relevantStates.add("all");

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java

@@ -46,7 +46,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Arrays.asList((Object)evalName);
     }
 }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java

@@ -0,0 +1,55 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+*
+* 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.gatk.tools.walkers.varianteval.stratifications;
+
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary;
+import htsjdk.variant.variantcontext.VariantContext;
+
+import java.util.*;
+
+/**
+ * Stratifies the eval RODs by each family in the eval ROD, as described by the pedigree.
+ *
+ * This allows the system to analyze each family separately.  This is particularly useful for the MendelianViolationEvaluator module.
+ */
+public class Family extends VariantStratifier {
+    @Override
+    public void initialize() {
+        states.addAll(getVariantEvalWalker().getFamilyNamesForStratification());
+    }
+
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
+        return Collections.singletonList((Object) familyName);
+    }
+
+    @Override
+    public Set<Class<? extends VariantEvaluator>> getIncompatibleEvaluators() {
+        return new HashSet<Class<? extends VariantEvaluator>>(Arrays.asList(VariantSummary.class));
+    }
+}

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java

@@ -43,7 +43,7 @@ public class Filter extends VariantStratifier {
         states.add("raw");
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList<Object> relevantStates = new ArrayList<Object>();
 
         relevantStates.add("raw");

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java

@@ -53,7 +53,7 @@ public class FunctionalClass extends VariantStratifier {
     }
 
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList<Object> relevantStates = new ArrayList<Object>();
 
         relevantStates.add("all");

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java

@@ -48,7 +48,7 @@ public class IndelSize extends VariantStratifier {
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null && eval.isIndel() && eval.isBiallelic()) {
             try {
                 int eventLength = 0;

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java

@@ -75,7 +75,7 @@ public class IntervalStratification extends VariantStratifier {
         states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval);
             IntervalTree<GenomeLoc> intervalTree = intervalTreeByContig.get(loc.getContig());

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java

@@ -54,7 +54,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
         }
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList<Object> relevantStates = new ArrayList<Object>();
         relevantStates.add("none");
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java

@@ -48,7 +48,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
         knowns = getVariantEvalWalker().getKnowns();
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (tracker != null && eval != null) {
             final Collection<VariantContext> knownComps = tracker.getValues(knowns, ref.getLocus());
             for ( final VariantContext c : knownComps ) {

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java

@@ -47,7 +47,7 @@ public class OneBPIndel extends VariantStratifier {
     }
 
     @Override
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null && eval.isIndel()) {
             for ( int l : eval.getIndelLengths() )
                 if ( Math.abs(l) > 1 )

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java

@@ -46,7 +46,7 @@ public class Sample extends VariantStratifier {
         states.addAll(getVariantEvalWalker().getSampleNamesForStratification());
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Collections.singletonList((Object) sampleName);
     }
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java

@@ -64,7 +64,8 @@ public class SnpEffPositionModifier extends VariantStratifier {
 			final String compName,
 			final VariantContext eval,
 			final String evalName,
-			final String sampleName)
+			final String sampleName,
+            final String FamilyName)
 	{
 		final List<Object> relevantStates = new ArrayList<Object>();
 		if (eval != null && eval.isVariant() && eval.hasAttribute(InfoFieldKey.EFFECT_KEY.getKeyName())) {

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java

@@ -48,7 +48,7 @@ public class TandemRepeat extends VariantStratifier {
     }
 
     @Override
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if ( eval == null || ! eval.isIndel() )
             return ALL;
         else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) {

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java

@@ -54,7 +54,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
 
     public abstract void initialize();
 
-    public abstract List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName);
+    public abstract List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName);
 
     // -------------------------------------------------------------------------------------
     //

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java

@@ -42,7 +42,7 @@ public class VariantType extends VariantStratifier {
             states.add(t.toString());
     }
 
-    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString());
     }
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.gatk.engine.samples.Sample;
 import org.broadinstitute.gatk.utils.commandline.RodBinding;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -255,6 +256,7 @@ public class VariantEvalUtils {
                         boolean byFilter,
                         boolean subsetBySample,
                         boolean trackPerSample,
+                        boolean trackPerFamily,
                         boolean mergeTracks) {
         if (tracker == null)
             return null;
@@ -270,9 +272,10 @@ public class VariantEvalUtils {
                 // First, filter the VariantContext to represent only the samples for evaluation
                 VariantContext vcsub = vc;
 
-                if (subsetBySample && vc.hasGenotypes())
+                if ((subsetBySample) && vc.hasGenotypes())
                     vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
 
+                //always add a mapping for all samples together
                 if ((byFilter || !vcsub.isFiltered())) {
                     addMapping(mapping, VariantEval.getAllSampleName(), vcsub);
                 }
@@ -287,6 +290,26 @@ public class VariantEvalUtils {
                         }
                     }
                 }
+                else if (vc.hasGenotypes() && trackPerFamily) {
+                    for (final String familyName : variantEvalWalker.getFamilyNamesForEvaluation()) {
+                        Set<String> familyMemberNames = new HashSet<>();
+                        //if the current stratification family name is "all", then add all the families to the VC for evaluation here
+                        if (familyName.equals(VariantEval.getAllFamilyName())) {
+                            familyMemberNames = variantEvalWalker.getSampleNamesForEvaluation();
+                        }
+                        else {
+                            Set<Sample> familyMembers = variantEvalWalker.getToolkit().getSampleDB().getFamily(familyName);
+                            for (final Sample s : familyMembers) {
+                                familyMemberNames.add(s.getID());
+                            }
+                        }
+                        VariantContext samplevc = getSubsetOfVariantContext(vc, familyMemberNames);
+
+                        if (byFilter || !samplevc.isFiltered()) {
+                            addMapping(mapping, familyName, samplevc);
+                        }
+                    }
+                }
             }
 
             if (mergeTracks && bindings.containsKey(firstTrack)) {