diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index e0121cb54..d755a7ecc 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -620,10 +620,6 @@ public class VariantContextUtils {
         return uniqify ? sampleName + "." + trackName : sampleName;
     }
 
-    public static VariantContext modifyLocation(VariantContext vc, GenomeLoc loc) {
-        return new VariantContext(vc.getSource(), loc.getContig(), loc.getStart(), loc.getStop(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
-    }
-
     /**
      * Returns a context identical to this with the REF and ALT alleles reverse complemented.
      *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 485af6261..2054c083d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -38,10 +38,8 @@ import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
@@ -136,9 +134,8 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         // update if necessary and write
         if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
             int difference = originalIndex - newCigar.getCigarElement(0).getLength();
-            GenomeLoc newLoc = getToolkit().getGenomeLocParser().createPotentiallyInvalidGenomeLoc(vc.getChr(), vc.getStart()-difference, vc.getEnd()-difference);
-            //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + newLoc);
-            VariantContext newVC = VariantContextUtils.modifyLocation(vc, newLoc);
+            VariantContext newVC = VariantContext.modifyLocation(vc, vc.getChr(), vc.getStart()-difference, vc.getEnd()-difference);
+            //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));
 
             int indelIndex = originalIndex-difference;
             byte[] newBases = new byte[indelLength];
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 5ece5f8fe..1749a13cf 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -28,9 +28,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -96,7 +94,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
                 vc = VariantContextUtils.reverseComplement(vc);
             }
 
-            vc = VariantContextUtils.modifyLocation(vc, getToolkit().getGenomeLocParser().createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
+            vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length);
             VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
 
             if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8ea108fe1..8cc405a21 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -366,19 +366,6 @@ public class GenomeLocParser {
         return contigInfo.getSequence(contigIndex).getSequenceName();
     }
 
-    /**
-     * create a genome loc, given the contig name, start, and stop
-     *
-     * @param contig the contig name
-     * @param start  the starting position
-     * @param stop   the stop position
-     *
-     * @return a new genome loc - but don't exception out if it is invalid
-     */
-    public GenomeLoc createPotentiallyInvalidGenomeLoc(String contig, final int start, final int stop) {
-        return new GenomeLoc(contig, getContigIndex(contig,false), start, stop);
-    }
-
     /**
      * create a genome loc, given the contig name, start, and stop
      *
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index 737a5910c..4f5be716a 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
+                 Arrays.asList("cc1b1ccb800b16abce2d177c181ede56"));
          executeTest("test b36 to hg19", spec);
     }