From 31fc64f82cc5fc87cc4764f4ce05c0f53ea00a76 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Mon, 14 Mar 2016 13:17:29 -0400
Subject: [PATCH 1/2] To address weird case with all hom-refs, but alt allele
 is present, skip AS_QD for all-ref sites and remove raw annotations whether
 or not they can be successfully finalized

---
 .../gatk/tools/walkers/annotator/AS_QualByDepth.java          | 2 ++
 .../gatk/tools/walkers/annotator/VariantAnnotatorEngine.java  | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
index e4c806e6a..8df281d72 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
@@ -172,6 +172,8 @@ public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnno
             return null;
 
         final List<Integer> standardDepth = getAlleleDepths(genotypes);
+        if (standardDepth == null) //all no-calls and homRefs
+            return null;
 
         //Parse the VC's allele-specific qual values
         List<Object> alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
index d62029fb3..e8394cec4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -357,9 +357,9 @@ public class VariantAnnotatorEngine {
             final Map<String, Object> annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC);
             if ( annotationsFromCurrentType != null ) {
                 infoAnnotations.putAll(annotationsFromCurrentType);
-                //clean up raw annotation data after annotations are finalized
-                infoAnnotations.remove(currentASannotation.getRawKeyName());
             }
+            //clean up raw annotation data after annotations are finalized
+            infoAnnotations.remove(currentASannotation.getRawKeyName());
         }
 
         // generate a new annotated VC

From 9ffdfeccd53e37428d5cbc711f53f561ed59cc95 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Tue, 15 Mar 2016 11:06:48 -0400
Subject: [PATCH 2/2] Add test case for fix

---
 .../gatk/tools/walkers/genotyper/GenotypingEngine.java   | 2 +-
 .../variantutils/GenotypeGVCFsIntegrationTest.java       | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
index 0a0debff9..6c1b28cb2 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
@@ -210,7 +210,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
      * @param vc                                 Input VC
      * @param model                              GL calculation model
      * @param inheritAttributesFromInputVC       Output VC will contain attributes inherited from input vc
-     * @return                                   VC with assigned genotypes
+     * @return                                   VC with assigned genotypes (may be null if QUAL<emit threshold or MLEAF==0)
      */
     protected VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker, final ReferenceContext refContext,
                                                  final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 049da9bba..2de0af25b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -612,6 +612,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
     }
 
+    @Test
+    public void testMonomorphicVCwithAlt() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V "
+                + privateTestDir + "monomorphicGVCwithAlt.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("080951cdb5d4903dd58b1e753b9378d5"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations", spec);
+    }
+
     @Test
     public void testFractionInformativeReads() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "