diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index bbe8cd05e..aa8a49175 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -321,7 +321,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 if (SELECT_RANDOM_NUMBER) {
                     randomlyAddVariant(++variantNumber, sub, ref.getBase());
                 }
-                else if (!SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom) {
+                else if (!SELECT_RANDOM_FRACTION || (!KEEP_AF_SPECTRUM && GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
                     vcfWriter.add(sub, ref.getBase());
                 }
                 else {