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 dc728ff6b..b3f77fc06 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
@@ -484,6 +484,9 @@ public class UnifiedGenotyperEngine {
 
         Map<String, AlignmentContext> stratifiedContexts = null;
 
+        if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
+            return null;
+
         if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) {
 
             if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
@@ -498,6 +501,7 @@ public class UnifiedGenotyperEngine {
                 stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
 
             } else {
+
                 // todo - tmp will get rid of extended events so this wont be needed
                 if (!rawContext.hasExtendedEventPileup())
                     return null;
@@ -515,9 +519,6 @@ public class UnifiedGenotyperEngine {
             }
         } else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
 
-            if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
-                return null;
-
             // stratify the AlignmentContext and cut by sample
             stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
index 3718345a4..70417889b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
@@ -135,6 +135,11 @@ public class NWaySAMFileWriter implements SAMFileWriter {
     
     public void addAlignment(SAMRecord samRecord) {
         final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
+        String rg = samRecord.getStringAttribute("RG");
+        if ( rg != null ) {
+            String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
+            samRecord.setAttribute("RG",rg_orig);
+        }
         writerMap.get(id).addAlignment(samRecord);
     }