diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
index 49b805fcd..40fa2a003 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
@@ -178,6 +178,14 @@ public abstract class LocusView extends LocusContextIterator implements View {
                 TraversalStatistics.nBadAlignments++;
                 result = true;
                 why = "No alignment start";
+            } else if (rec.getAlignmentEnd() != -1 && rec.getAlignmentEnd() < rec.getAlignmentStart() ) {
+                TraversalStatistics.nBadAlignments++;
+                result = true;
+                why = "Alignment ends before it starts";
+            } else if (rec.getAlignmentStart() != -1 && rec.getAlignmentBlocks().size() == 0) {
+                TraversalStatistics.nBadAlignments++;
+                result = true;
+                why = "Alignment cigar string is invalid";
             } else if (rec.getDuplicateReadFlag()) {
                 TraversalStatistics.nDuplicates++;
                 result = true;