diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
index 28cfdd5cd..8fbd37e30 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
@@ -47,8 +47,10 @@ import java.util.List;
  * <p>
  * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
  * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
- * Note that if there are multiple variants at a site, it chooses one of them randomly.
- * Also note that this tool works only for SNPs and for simple indels (but not for things like complex substitutions).
+ * Several important notes:
+ * 1) if there are multiple variants that start at a site, it chooses one of them randomly.
+ * 2) when there are overlapping indels (but with different start positions) only the first will be chosen.
+ * 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions).
  * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
  *
  * <h2>Input</h2>
@@ -103,7 +105,7 @@ public class FastaAlternateReference extends FastaReference {
         String refBase = String.valueOf((char)ref.getBase());
 
         // Check to see if we have a called snp
-        for ( VariantContext vc : tracker.getValues(variants) ) {
+        for ( VariantContext vc : tracker.getValues(variants, ref.getLocus()) ) {
             if ( vc.isFiltered() )
                 continue;