diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index e82cf5245..298a7e38c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -66,7 +66,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         boolean failed = false;
         byte[] recordRef = vc.getReference().getBases();
         for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
-            if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) {
+            if ( recordRef[i] != ref[i + (vc.isPointEvent() ? 0 : 1)] ) {
                 failed = true;
                 break;
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index f2dc051d7..4c23fbae7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -92,14 +92,14 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         if ( toInterval != null ) {
             // check whether the strand flips, and if so reverse complement everything
             // TODO -- make this work for indels (difficult because the 'previous base' context needed will be changing based on indel type/size)
-            if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && (vc.isSNP() || !vc.isVariant()) ) {
+            if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) {
                 vc = VariantContextUtils.reverseComplement(vc);
             }
 
             vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
             VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
 
-            if ( originalVC.isVariant() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
+            if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
                 logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
                         originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),
                         originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0)));