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 92549b821..28cfdd5cd 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
@@ -47,7 +47,8 @@ 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 takes the first one seen.
+ * 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).
  * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
  *
  * <h2>Input</h2>