diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
index 0b28416e4..6571d1a40 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
@@ -6,19 +6,20 @@ import java.util.List;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodSAMPileup;
-import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
+import org.broadinstitute.sting.gatk.refdata.Genotype;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.playground.utils.TrioConcordanceRecord;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord, TrioConcordanceRecord> {
 
-	@Argument(fullName="conf_cutoff", shortName="X",required=true ) public Double CONF_CUTOFF;
+	@Argument(fullName="consensus_cutoff", shortName="XC",required=true ) public Double CONS_CUTOFF;
+	@Argument(fullName="snp_cutoff", shortName="XS",required=true ) public Double SNP_CUTOFF;
+	@Argument(fullName="indel_cutoff", shortName="XI",required=true ) public Double INDEL_CUTOFF;
 	
 	private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);	
-	
+	private final static String star = new String("*");
 	
 	@Override
 	public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
@@ -27,15 +28,33 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 		
 //		String outLine = new String(context.getLocation() + " REF: "+ref + " RODS:" + rodData.getAllRods().size());
 		
-		AllelicVariant mom = (rodSAMPileup)rodData.lookup("mother", null);
-		AllelicVariant dad = (rodSAMPileup)rodData.lookup("father", null);
-		AllelicVariant kid = (rodSAMPileup)rodData.lookup("daughter", null);
+		Genotype mom = (rodSAMPileup)rodData.lookup("mother", null);
+		Genotype dad = (rodSAMPileup)rodData.lookup("father", null);
+		Genotype kid = (rodSAMPileup)rodData.lookup("daughter", null);
 		
-		if ( hasCall(mom)) t.mom_assessed = 1;
-		if ( hasCall(dad)) t.dad_assessed = 1;
-		if ( hasCall(kid)) t.kid_assessed = 1;
+		if ( hasCall(mom)) {
+			t.mom_assessed = 1;
+			if ( mom.isReference() ) t.mom_ref = 1;
+			else if ( mom.isSNP() ) t.mom_snp = 1;
+			else if ( mom.isIndel() ) t.mom_indel = 1;
+		}
+
+		if ( hasCall(dad)) {
+			t.dad_assessed = 1;
+			if ( dad.isReference() ) t.dad_ref = 1;
+			else if ( dad.isSNP() ) t.dad_snp = 1;
+			else if ( dad.isIndel() ) t.dad_indel = 1;
+		}
 		
-		if ( hasCall(mom) && mom.isIndel() ) System.out.println("GOT INDEL: "+mom.toString());
+		if ( hasCall(kid)) {
+			t.kid_assessed = 1;
+			if ( kid.isReference() ) t.kid_ref = 1;
+			else if ( kid.isSNP() ) t.kid_snp = 1;
+			else if ( kid.isIndel() ) t.kid_indel = 1;
+		}
+		
+
+		//		if ( hasCall(mom) && mom.isIndel() ) System.out.println("GOT INDEL: "+mom.toString());
 		
 		if (( t.mom_assessed + t.dad_assessed + t.kid_assessed) != 3 ) return t; // at least one person is not called; nothing to do, bail out
 			
@@ -43,10 +62,6 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 			
         t.assessed_loci = 1;
 			
-		if ( ! mom.isBiallelic() || ! dad.isBiallelic() || ! kid.isBiallelic() ) {
-			t.non_biallelic = 1; // we currently ignore non-biallelic sites
-			return t;
-		}
 		
 		// ok, we got a call and it is biallelic (at most)
 		
@@ -55,40 +70,97 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 			return t;
 		}
 
-		// by now we know that there's a SNP
+		// by now we know that there's a SNP or an indel: at least one of the individuals is non-ref
 		
-		String kid_allele_1 = kid.getGenotype().get(0);
-		String kid_allele_2 = kid.getGenotype().get(1);
-		List<String> mom_alleles = mom.getGenotype();
-		List<String> dad_alleles = dad.getGenotype();
+		String kid_allele_1 = kid.getFWDAlleles().get(0);
+		String kid_allele_2 = kid.getFWDAlleles().get(1);
+		List<String> mom_alleles = mom.getFWDAlleles();
+		List<String> dad_alleles = dad.getFWDAlleles();
 		
-		// kid must have one allele from mom and one allele from dad if it's not X chromosome!
+		if ( ! mom.isIndel() && ! dad.isIndel() && ! kid.isIndel() ) {
+			// individuals have SNPs (any member of the trio is ok, we'll check for consistency in a sec), but no indels at the site:
 		
-		if ( mom_alleles.contains(kid_allele_1) && dad_alleles.contains(kid_allele_2) ||
-				mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
-			t.consistent_snp = 1;
+			// warning: no special processing for X/Y chromosomes yet; not an issue for daughter
+
+			if ( ! mom.isBiallelic() || ! dad.isBiallelic() || ! kid.isBiallelic() ) {
+				t.non_biallelic_snp = 1; // we currently ignore non-biallelic sites
+				return t;
+			}
 			
+			
+			if ( mom_alleles.contains(kid_allele_1) && dad_alleles.contains(kid_allele_2) ||
+					mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
+				t.consistent_snp = 1;
+				
 //			logger.info("consistent SNP at "+context.getLocation() + 
 //					"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
 //					dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
 //					kid_allele_1+"/" +kid_allele_2  
 //					);
+			} else {
+				// we are inconsistent. let's see what happened:
+				if ( kid.isSNP() && ! mom.isSNP() && ! dad.isSNP() ) t.missing_snp_in_parents = 1;
+				if ( ! kid.isSNP() && ( mom.isSNP() && mom.isHom() || dad.isSNP() && dad.isHom() ) ) t.missing_snp_in_kid = 1;
+				
+				t.inconsistent_snp = 1;
+				logger.info("INconsistent SNP at "+context.getLocation() + 
+						"("+ref+")  mom:" + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " dad: " +
+						dad_alleles.get(0)+"/" +dad_alleles.get(1) + " kid: " +
+						kid_allele_1+"/" +kid_allele_2  
+						);
+			}
 			return t;
-	    }
+		}
+
+		if ( ! mom.isSNP() && ! dad.isSNP() && ! kid.isSNP() ) {
+			// individuals have indels (any member of the trio is ok, we'll check for consistency in a seq), but no indels at the site:
+			
+			// warning: no special processing for X/Y chromosomes yet; not an issue for daughter
+
+			if ( ! mom.isBiallelic() || ! dad.isBiallelic() || ! kid.isBiallelic() ) {
+				t.non_biallelic_indel = 1; // we currently ignore non-biallelic sites
+				return t;
+			}
+
+			if ( mom_alleles.contains(kid_allele_1) && dad_alleles.contains(kid_allele_2) ||
+						mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
+					t.consistent_indels = 1;
+				
+					logger.info("consistent INDEL at "+context.getLocation() + 
+							"("+ref+")  mom:" + genotypeString(mom)+ " dad: " +
+							genotypeString(dad) + " kid: " +
+							genotypeString(kid)  
+							);
+							
+			} else {
+				  if ( kid.isIndel() && ! mom.isIndel() && ! dad.isIndel() ) t.missing_indels_in_parents = 1;
+				  if ( ! kid.isIndel() && ( mom.isIndel() && mom.isHom() || dad.isIndel() && dad.isHom() ) ) t.missing_indels_in_kid = 1;
+
+				  t.inconsistent_indels = 1;
+					logger.info("INconsistent INDEL at "+context.getLocation() + 
+							"("+ref+")  mom:" + genotypeString(mom)+ " dad: " +
+							genotypeString(dad) + " kid: " +
+							genotypeString(kid)  
+							);
+			}
+			return t;
+		}
 		
-		// snp is inconsistent
-		
-		t.inconsistent_snp = 1;
-		logger.info("INconsistent SNP at "+context.getLocation() + 
-				"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
-				dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
-				kid_allele_1+"/" +kid_allele_2  
-				);
+		t.unclassified_events = 1;
 		
 		return t;
 		
 	}
 
+	protected String alleleString(Genotype g, int n) {
+		if ( g.getFWDAlleles().get(n).length() == 0 ) return star;
+		return g.getFWDAlleles().get(n);
+	}
+	
+	protected String genotypeString(Genotype g) {
+		return alleleString(g, 0) +"/"+alleleString(g, 1);
+	}
+
 	@Override
 	public TrioConcordanceRecord reduce(TrioConcordanceRecord value, TrioConcordanceRecord sum) {
 		
@@ -101,24 +173,41 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 		return new TrioConcordanceRecord();
 	}
 
-	boolean hasCall(AllelicVariant av) {
-		if ( av == null ) return false; // there's no call if there's no rod data available, duh!
-		if ( av.isReference() ) return av.getConsensusConfidence() >= CONF_CUTOFF ;
-		else return av.getVariationConfidence() >= CONF_CUTOFF;
+	boolean hasCall(Genotype g) {
+		if ( g == null ) return false; // there's no call if there's no rod data available, duh!
+		if ( g.isReference() ) return g.getConsensusConfidence() >= CONS_CUTOFF ;
+		else {
+			if ( g.isSNP() ) return g.getVariantConfidence() >= SNP_CUTOFF;
+			else return Math.max(g.getConsensusConfidence(),g.getVariantConfidence()) >= INDEL_CUTOFF;
+		}
 		
 	}
 	
-	protected String shortLine(AllelicVariant av) {
+	/*
+	protected String shortLine(Genotype av) {
 		
 		if ( av == null )  return new String( "<NULL>");
 		
 		if ( av.isReference() ) return new String ("*");
 		
-		if ( av.isSNP() ) return av.getAltBasesFWD();
-		if ( av.isInsertion() ) return new String('+'+av.getAltBasesFWD());
-		if ( av.isDeletion() ) return new String('-'+av.getRefBasesFWD());
-		if ( av.isIndel() ) return new String('?'+av.getAltBasesFWD());
+		List<String> alleles = av.getFWDAlleles();
+		
+		if ( av.isSNP() ) {
+            if  ( alleles.get(0).charAt(0) == av.getRef() ) return alleles.get(1);
+            else return alleles.get(0);
+		}
+		if ( av.isInsertion() ) {
+            if ( alleles.get(0).length() == 0 ) return new String('+'+alleles.get(1));
+            else return new String('+'+alleles.get(0));
+		}
+		if ( av.isDeletion() ) {
+            if ( alleles.get(0).length() == 0 ) return new String ('-'+alleles.get(0));
+            else return new String('-'+alleles.get(1));
+		}
+		if ( av.isIndel() ) {
+			return new String('?'+alleles.get(0));
+		}
 		return new String("<missing data!!!>");
 	}
-	
+	*/
 }