diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index d7e163917..1ee658f5c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -58,6 +58,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
     private boolean DEBUG = false;
 
+    private boolean ignoreSNPAllelesWhenGenotypingIndels = false;
+
     private PairHMMIndelErrorModel pairModel;
 
     private static ThreadLocal<HashMap<PileupElement,LinkedHashMap<Allele,Double>>> indelLikelihoodMap =
@@ -111,7 +113,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         DEBUG = UAC.OUTPUT_DEBUG_INDEL_INFO;
 
         haplotypeMap = new LinkedHashMap<Allele,Haplotype>();
-
+        ignoreSNPAllelesWhenGenotypingIndels = UAC.IGNORE_SNP_ALLELES;
     }
 
 
@@ -333,8 +335,19 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                      return null;
 
                 alleleList.clear();
-                for (Allele a : vc.getAlleles())
-                    alleleList.add(a);
+                if (ignoreSNPAllelesWhenGenotypingIndels) {
+                    // if there's an allele that has same length as the reference (i.e. a SNP or MNP), ignore it and don't genotype it
+                    for (Allele a : vc.getAlleles())
+                        if (a.isNonReference() && a.getBases().length == vc.getReference().getBases().length)
+                            continue;
+                        else
+                            alleleList.add(a);
+
+                }
+                else {
+                    for (Allele a : vc.getAlleles())
+                        alleleList.add(a);
+                }
 
             }
             else {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 51fe985bb..1045ca371 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -124,6 +124,11 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "exactCalculation", shortName = "exactCalculation", doc = "expt", required = false)
     public ExactAFCalculationModel.ExactCalculation EXACT_CALCULATION_TYPE = ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL;
 
+    @Hidden
+     @Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
+    public boolean IGNORE_SNP_ALLELES = false;
+
+
     @Deprecated
     @Argument(fullName="output_all_callable_bases", shortName="all_bases", doc="Please use --output_mode EMIT_ALL_SITES instead" ,required=false)
     private Boolean ALL_BASES_DEPRECATED = false;   
@@ -165,6 +170,7 @@ public class UnifiedArgumentCollection {
         uac.COVERAGE_AT_WHICH_TO_ABORT = COVERAGE_AT_WHICH_TO_ABORT;
         uac.dovit = dovit;
         uac.GSA_PRODUCTION_ONLY = GSA_PRODUCTION_ONLY;
+        uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;
         
         return uac;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index a3bc4d3df..0131b1bc9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -240,7 +240,7 @@ public class VariantDataManager {
         datum.consensusCount = 0;
         for( final TrainingSet trainingSet : trainingSets ) {
             for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) {
-                if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP()) || (evalVC.isIndel() && trainVC.isIndel())) && (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {
+                if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP())) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed())) && (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {
                     datum.isKnown = datum.isKnown || trainingSet.isKnown;
                     datum.atTruthSite = datum.atTruthSite || trainingSet.isTruth;
                     datum.atTrainingSite = datum.atTrainingSite || trainingSet.isTraining;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 3c76b48f5..f8cfbf17f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -194,7 +194,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     public static boolean checkRecalibrationMode( final VariantContext vc, final VariantRecalibratorArgumentCollection.Mode mode ) {
         return mode == VariantRecalibratorArgumentCollection.Mode.BOTH ||
                 (mode == VariantRecalibratorArgumentCollection.Mode.SNP && vc.isSNP()) ||
-                (mode == VariantRecalibratorArgumentCollection.Mode.INDEL && vc.isIndel());
+	    (mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed()));
     }
 
     //---------------------------------------------------------------------------------------------------------------