diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
index 1942fc19a..37f919417 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
@@ -115,10 +115,10 @@ public class CountingFilteringIterator implements CloseableIterator<SAMRecord> {
     public void close() {
         CloserUtil.close(iterator);
 
+        for ( final CountingReadFilter filter : filters )
+            privateRuntimeMetrics.setFilterCount(filter.readFilter.getClass().getSimpleName(), filter.counter);
         // update the global metrics with all the data we collected here
         globalRuntimeMetrics.incrementMetrics(privateRuntimeMetrics);
-        for ( final CountingReadFilter filter : filters )
-            globalRuntimeMetrics.setFilterCount(filter.readFilter.getClass().getSimpleName(), filter.counter);
     }
 
     /**