VariantAnnotator fails when the variant contains too many alleles

src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java

@@ -478,4 +478,11 @@ public static final class ValidationFailure extends UserException {
 
         public ValidationFailure(String message) { super(message); }
     }
+
+    public static final class WarnableAnnotationFailure extends UserException {
+        private static final long serialVersionUID = 0L;
+
+        public WarnableAnnotationFailure(String message) { super(message); }
+
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java

@@ -14,6 +14,7 @@
 import org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData;
+import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods;
 import org.broadinstitute.hellbender.utils.haplotype.Haplotype;
@@ -365,7 +366,12 @@ public VariantContext annotateContext(final VariantContext vc,
         final VariantContext annotated = builder.attributes(infoAnnotMap).make();
 
         // annotate db occurrences
-        return variantOverlapAnnotator.annotateOverlaps(features, variantOverlapAnnotator.annotateRsID(features, annotated));
+        try {
+            return variantOverlapAnnotator.annotateOverlaps(features, variantOverlapAnnotator.annotateRsID(features, annotated));
+        } catch (UserException.WarnableAnnotationFailure e) {
+            logger.warn("failed to apply variantOverlapAnnotator to VC at " + IntervalUtils.locatableToString(annotated) + ": " + e.getMessage());
+            return annotated;
+        }
     }
 
     private Map<String, Object> addInfoAnnotations(VariantContext vc, FeatureContext features, ReferenceContext ref,

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.genotyper;
 
 import org.broadinstitute.hellbender.exceptions.GATKException;
+import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.MathUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.apache.logging.log4j.LogManager;
@@ -273,7 +274,7 @@ private synchronized void calculateGenotypeCountsUsingTablesAndValidate(final in
 
         if (calculateGenotypeCountUsingTables(ploidy, alleleCount) == GENOTYPE_COUNT_OVERFLOW) {
             final double largeGenotypeCount = Math.pow(10, MathUtils.log10BinomialCoefficient(ploidy + alleleCount - 1, alleleCount - 1));
-            throw new IllegalArgumentException(String.format("the number of genotypes is too large for ploidy %d and allele %d: approx. %.0f", ploidy, alleleCount, largeGenotypeCount));
+            throw new UserException.WarnableAnnotationFailure(String.format("the number of genotypes is too large for ploidy %d and allele %d: approx. %.0f", ploidy, alleleCount, largeGenotypeCount));
         }
     }
 
@@ -368,7 +369,7 @@ public int genotypeCount(final int ploidy, final int alleleCount) {
         final int result = calculateGenotypeCountUsingTables(ploidy, alleleCount);
         if (result == GENOTYPE_COUNT_OVERFLOW) {
             final double largeGenotypeCount = Math.pow(10, MathUtils.log10BinomialCoefficient(ploidy + alleleCount - 1, alleleCount - 1));
-            throw new IllegalArgumentException(String.format("the number of genotypes is too large for ploidy %d and allele %d: approx. %.0f", ploidy, alleleCount, largeGenotypeCount));
+            throw new UserException.WarnableAnnotationFailure(String.format("the number of genotypes is too large for ploidy %d and allele %d: approx. %.0f", ploidy, alleleCount, largeGenotypeCount));
         }
         return result;
     }

src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeLikelihoodCalculatorsUnitTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.genotyper;
 
 import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -75,7 +76,7 @@ public void testInstanceNewInstance(int ploidy, int alleleCount, int expected) t
         }
     }
 
-    @Test(expectedExceptions = IllegalArgumentException.class)
+    @Test(expectedExceptions = UserException.WarnableAnnotationFailure.class)
     public void testGenotypeCountOverflow() throws Exception {
         final int genotypeCount = new GenotypeLikelihoodCalculators().genotypeCount(10_000, 10_000);
     }