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 08633d5bb..f02789b9a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -87,4 +87,11 @@ public class UnifiedArgumentCollection {
 
     @Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false)
     public double MINIMUM_ALLELE_FREQUENCY = 1e-8;
+
+    // Mark's filtering arguments
+    //@Argument(fullName = "minBaseQualityScore", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
+    public Integer MIN_BASE_QUALTY_SCORE = -1;
+
+    //@Argument(fullName = "minMappingQualityScore", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
+    public Integer MIN_MAPPING_QUALTY_SCORE = -1;
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 617e6b7b8..aca57e18b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.alignment.Alignment;
 
 import net.sf.samtools.SAMReadGroupRecord;
 
@@ -196,20 +197,21 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
      *
      * @param tracker the meta data tracker
      * @param refContext the reference base
-     * @param context contextual information around the locus
+     * @param rawContext contextual information around the locus
      */
-    public Pair<VariationCall, List<Genotype>> map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext context) {
+    public Pair<VariationCall, List<Genotype>> map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
         char ref = Character.toUpperCase(refContext.getBase());
         if ( !BaseUtils.isRegularBase(ref) )
             return null;
 
         // an optimization to speed things up when there is no coverage or when overly covered
-        if ( context.getPileup().size() == 0 ||
-             (UAC.MAX_READS_IN_PILEUP > 0 && context.getPileup().size() > UAC.MAX_READS_IN_PILEUP) )
+        if ( rawContext.getPileup().size() == 0 ||
+             (UAC.MAX_READS_IN_PILEUP > 0 && rawContext.getPileup().size() > UAC.MAX_READS_IN_PILEUP) )
             return null;
 
         // are there too many deletions in the pileup?
-        ReadBackedPileup pileup = context.getPileup();
+        ReadBackedPileup pileup = rawContext.getPileup().getBaseAndMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE, UAC.MIN_MAPPING_QUALTY_SCORE);
+        AlignmentContext context = new AlignmentContext(rawContext.getLocation(), pileup);
         if ( isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) &&
              (double)pileup.getPileupWithoutMappingQualityZeroReads().getNumberOfDeletions() / (double)(pileup.size() - pileup.getNumberOfMappingQualityZeroReads()) > UAC.MAX_DELETION_FRACTION )
             return null;
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
index 4ae03cde0..d9a4eeffa 100755
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
@@ -153,6 +153,8 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
      * @return
      */
     public ReadBackedPileup getPileupWithoutMappingQualityZeroReads() {
+        // todo -- eric, this can be more efficient, FYI
+
         if ( getNumberOfMappingQualityZeroReads() > 0 ) {
             List<SAMRecord> newReads = new ArrayList<SAMRecord>();
             List<Integer> newOffsets = new ArrayList<Integer>();
@@ -169,6 +171,17 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
         }
     }
 
+    public ReadBackedPileup getBaseAndMappingFilteredPileup( int minBaseQ, int minMapQ ) {
+        ArrayList<PileupElement> filteredPileup = new ArrayList<PileupElement>();
+
+        for ( PileupElement p : pileup ) {
+            if ( p.getRead().getMappingQuality() >= minMapQ && p.getQual() >= minBaseQ ) {
+                filteredPileup.add(p);
+            }
+        }
+
+        return new ReadBackedPileup(loc, filteredPileup);
+    }
     /**
      * Returns a pileup randomly downsampled to the desiredCoverage.
      *