Fix for PossibleDeNovo annotation to work without Genotype Likelihoods (

#7662) * PossibleDeNovo annotation works on VCF without PLs
broadinstitute · Feb 8, 2022 · 0d4897f · 0d4897f
1 parent f3ea606
commit 0d4897f
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/PossibleDeNovo.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/PossibleDeNovo.java
@@ -105,7 +105,7 @@ public Map<String, Object> annotate(final ReferenceContext ref,
         final List<String> lowConfDeNovoChildren = new ArrayList<>();
         for (final Trio trio : trioSet) {
             if (vc.isBiallelic() &&
-                PossibleDeNovo.contextHasTrioLikelihoods(vc, trio) &&
+                PossibleDeNovo.contextHasTrioGQs(vc, trio) &&
                 mendelianViolation.isViolation(trio.getMother(), trio.getFather(), trio.getChild(), vc) &&
                 mendelianViolation.getParentsRefRefChildHet() > 0) {
 
@@ -135,14 +135,14 @@ public Map<String, Object> annotate(final ReferenceContext ref,
         return attributeMap;
     }
 
-    private static boolean contextHasTrioLikelihoods(final VariantContext vc, final Trio trio) {
+    private static boolean contextHasTrioGQs(final VariantContext vc, final Trio trio) {
         final String mom = trio.getMaternalID();
         final String dad = trio.getPaternalID();
         final String kid = trio.getChildID();
 
-        return   (!mom.isEmpty() && vc.hasGenotype(mom) && vc.getGenotype(mom).hasLikelihoods())
-              && (!dad.isEmpty() && vc.hasGenotype(dad) && vc.getGenotype(dad).hasLikelihoods())
-              && (!kid.isEmpty() && vc.hasGenotype(kid) && vc.getGenotype(kid).hasLikelihoods());
+        return   (!mom.isEmpty() && vc.hasGenotype(mom) && vc.getGenotype(mom).hasGQ())
+              && (!dad.isEmpty() && vc.hasGenotype(dad) && vc.getGenotype(dad).hasGQ())
+              && (!kid.isEmpty() && vc.hasGenotype(kid) && vc.getGenotype(kid).hasGQ());
     }
 
 }
diff --git a/...st/java/org/broadinstitute/hellbender/tools/walkers/annotator/PossibleDeNovoUnitTest.java b/...st/java/org/broadinstitute/hellbender/tools/walkers/annotator/PossibleDeNovoUnitTest.java
@@ -117,6 +117,13 @@ public Object[][] deNovo() {
         tests.add(new Object[]{gNo, gNo, g11, false});
         tests.add(new Object[]{gNo, gNo, gNo, false});
 
+        final Genotype g00NoPl = new GenotypeBuilder("2", homRef).DP(10).GQ(GQ30).make();
+        final Genotype g01NoPl = new GenotypeBuilder("1", het).DP(10).GQ(GQ30).make();
+        final Genotype g11NoPl = new GenotypeBuilder("3", homVar).DP(10).GQ(GQ30).make();
+
+        tests.add(new Object[]{g00NoPl, g01NoPl, g11NoPl, false});
+        tests.add(new Object[]{g00NoPl, g00NoPl, g01NoPl, true});
+
         return tests.toArray(new Object[][]{});
     }