diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 5a269087c..5f84f62ec 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -205,6 +205,12 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      *
      **/
     public void initialize() {
+        // warn the user for misusing EMIT_ALL_SITES
+        if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
+                UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY &&
+                UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.SNP )
+            logger.warn("Note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode");
+        
         // get all of the unique sample names
         Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index ee5aed3e5..ba4b22445 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -54,8 +54,9 @@ public class UnifiedGenotyperEngine {
         EMIT_VARIANTS_ONLY,
         /** produces calls at variant sites and confident reference sites */
         EMIT_ALL_CONFIDENT_SITES,
-        /** produces calls at any callable site regardless of confidence; this argument is intended for point
-         * mutations (SNPs) only and while some indel calls may be produced they are by no means comprehensive */
+        /** produces calls at any callable site regardless of confidence; this argument is intended only for point
+         * mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by
+         * no means produce a comprehensive set of indels in DISCOVERY mode */
         EMIT_ALL_SITES
     }