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 4010d70bf..ce900927e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -85,7 +84,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         final Interval toInterval = liftOver.liftOver(fromInterval);
 
         if ( toInterval != null ) {
-            vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getEnd()));
+            vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getEnd()));
             writer.add(vc, ref.getBase());
             successfulIntervals++;
         } else {
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 4db6f3611..a947256d6 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -407,6 +407,20 @@ public class GenomeLocParser {
         return exceptionOnInvalidGenomeLoc(new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig,true), start, stop));
     }
 
+    /**
+     * 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 static GenomeLoc createPotentiallyInvalidGenomeLoc(String contig, final long start, final long stop) {
+        checkSetup();
+        return new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig,false), start, stop);
+    }
+
     /**
      * create a genome loc, given the contig index, start, and stop
      *