diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index c97f0bf02..303a2871a 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -242,6 +242,32 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testRemoveMLE--" + testFile, spec);
     }
 
+    @Test
+    public void testKeepOriginalAC() {
+        String testFile = privateTestDir + "vcfexample.loseAlleleInSelection.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants --keepOriginalAC -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("ad7e8b25e431a3229a78cec063876559")
+        );
+
+        executeTest("testKeepOriginalAC--" + testFile, spec);
+    }
+
+    @Test
+    public void testKeepOriginalACAndENV() {
+        String testFile = privateTestDir + "vcfexample.loseAlleleInSelection.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants --keepOriginalAC -env -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("e9b8292212545684cdb163423329ee7e")
+        );
+
+        executeTest("testKeepOriginalACAndENV--" + testFile, spec);
+    }
+
     @Test
     public void testMultipleRecordsAtOnePosition() {
         String testFile = privateTestDir + "selectVariants.onePosition.vcf";
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 52c1acd2d..02c8ed8d8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -406,8 +406,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
 
         if (KEEP_ORIGINAL_CHR_COUNTS) {
-            headerLines.add(new VCFInfoHeaderLine("AC_Orig", 1, VCFHeaderLineType.Integer, "Original AC"));
-            headerLines.add(new VCFInfoHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF"));
+            headerLines.add(new VCFInfoHeaderLine("AC_Orig", VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC"));
+            headerLines.add(new VCFInfoHeaderLine("AF_Orig", VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF"));
             headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
         }
         headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
@@ -670,7 +670,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         GenotypesContext newGC = sub.getGenotypes();
 
         // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate)
-        if ( vc.getAlleles().size() != sub.getAlleles().size() )
+        final boolean lostAllelesInSelection = vc.getAlleles().size() != sub.getAlleles().size();
+        if ( lostAllelesInSelection )
             newGC = GATKVariantContextUtils.stripPLsAndAD(sub.getGenotypes());
 
         // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
@@ -697,15 +698,22 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         builder.genotypes(newGC);
 
-        addAnnotations(builder, sub);
+        addAnnotations(builder, sub, lostAllelesInSelection);
 
         return builder.make();
     }
 
-    private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC) {
+    /*
+     * Add annotations to the new VC
+     *
+     * @param builder     the new VC to annotate
+     * @param originalVC  the original -- but post-selection -- VC
+     * @param lostAllelesInSelection  true if the original (pre-selection) VC has more alleles than the new one
+     */
+    private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC, final boolean lostAllelesInSelection) {
         if ( fullyDecode ) return; // TODO -- annotations are broken with fully decoded data
 
-        if (KEEP_ORIGINAL_CHR_COUNTS) {
+        if ( KEEP_ORIGINAL_CHR_COUNTS && !lostAllelesInSelection ) {
             if ( originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
                 builder.attribute("AC_Orig", originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
             if ( originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )