diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
index ca2988d81..aa1b00f5f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
@@ -106,10 +106,11 @@ import java.util.*;
  *   -o cohort.g.vcf
  * </pre>
  *
- * <h3>Caveat</h3>
+ * <h3>Caveats</h3>
  * <p>Only gVCF files produced by HaplotypeCaller (or CombineGVCFs) can be used as input for this tool. Some other
  * programs produce files that they call gVCFs but those lack some important information (accurate genotype likelihoods
  * for every position) that GenotypeGVCFs requires for its operation.</p>
+ * <p>If the gVCF files contain allele specific annotations, add -G Standard -G AS_Standard to the command line.</p>
  *
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
index b298ba25c..da9b8358a 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
@@ -122,10 +122,11 @@ import java.util.*;
  *   -o output.vcf
  * </pre>
  *
- * <h3>Caveat</h3>
+ * <h3>Caveats</h3>
  * <p>Only gVCF files produced by HaplotypeCaller (or CombineGVCFs) can be used as input for this tool. Some other
  * programs produce files that they call gVCFs but those lack some important information (accurate genotype likelihoods
  * for every position) that GenotypeGVCFs requires for its operation.</p>
+ * <p>If the gVCF files contain allele specific annotations, add -G Standard -G AS_Standard to the command line.</p>
  *
  * <h3>Special note on ploidy</h3>
  * <p>This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
index 05c0a930d..7443c8d8d 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
@@ -78,6 +78,8 @@ public class ReferenceConfidenceVariantContextMerger {
 
     private final static Logger logger = Logger.getLogger(ReferenceConfidenceVariantContextMerger.class);
 
+    static final String ADD_AS_STANDARD_MSG = " Add -G Standard -G AS_Standard to the command to annotate in the final VC.";
+
     private static Comparable combineAnnotationValues( final List<Comparable> array ) {
         return MathUtils.median(array); // right now we take the median but other options could be explored
     }
@@ -244,7 +246,9 @@ public class ReferenceConfidenceVariantContextMerger {
                     }
 
                 } catch (final NumberFormatException e) {
-                    logger.warn("WARNING: remaining (non-reducible) annotations are assumed to be ints or doubles or booleans, but " + value.getRawData() + " doesn't parse and will not be annotated in the final VC.");
+                    final String baseMsg = "Remaining (non-reducible) annotations are assumed to be ints or doubles, but " + value.getRawData() + " doesn't parse and will not be annotated in the final VC.";
+                    final String msg = value.getRawData().contains("|") ? baseMsg + ADD_AS_STANDARD_MSG : baseMsg;
+                    logger.warn(msg);
                 }
             }
             parsedAnnotations.put(currentData.getKey(),annotationValues);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
index 286ef6604..6945d82b3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
+import org.apache.commons.io.FileUtils;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.broadinstitute.gatk.engine.GATKVCFUtils;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -58,6 +59,7 @@ import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 
@@ -282,6 +284,18 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
         executeTest("testAlleleSpecificAnnotations", spec);
     }
 
+    @Test
+    public void testMissingAlleleSpecificAnnotationGroup() throws IOException {
+        final File logFile = createTempFile("testMissingAlleleSpecificAnnotationGroup.log", ".tmp");
+        final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.chr20snippet.g.vcf -log " +
+                logFile.getAbsolutePath();
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList(""));
+        spec.disableShadowBCF();
+        executeTest("testMissingAlleleSpecificAnnotationGroup", spec);
+        Assert.assertTrue(FileUtils.readFileToString(logFile).contains(ReferenceConfidenceVariantContextMerger.ADD_AS_STANDARD_MSG));
+    }
+
     @Test
     public void testASMateRankSumAnnotation() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest -V "
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 2531fb570..3639f236f 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
@@ -604,6 +604,16 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         executeTest("testAlleleSpecificAnnotations", spec);
     }
 
+    @Test
+    public void testMissingAlleleSpecificAnnotationGroup() throws IOException {
+        final File logFile = createTempFile("testMissingAlleleSpecificAnnotationGroup.log", ".tmp");
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header --disableDithering -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12892.AS.chr20snippet.g.vcf -log " + logFile.getAbsolutePath();
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList(""));
+        spec.disableShadowBCF();
+        executeTest("testMissingAlleleSpecificAnnotationGroup", spec);
+    }
+
     @Test
     public void testASMateRankSumAnnotation() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V "