diff --git a/java/src/org/broadinstitute/sting/gatk/filters/BadCigarReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/BadCigarReadFilter.java
new file mode 100755
index 000000000..a91acb04c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/filters/BadCigarReadFilter.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2009 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.*;
+
+/**
+ * Filter out reads with wonky cigar strings.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
+
+public class BadCigarReadFilter implements SamRecordFilter {
+
+    public boolean filterOut(final SAMRecord rec) {
+        Cigar c = rec.getCigar();
+        boolean lastElementWasIndel = false;
+        for ( CigarElement ce : c.getCigarElements() ) {
+            if ( ce.getOperator() == CigarOperator.D || ce.getOperator() == CigarOperator.I ) {
+                if ( lastElementWasIndel )
+                    return true;
+                lastElementWasIndel = true;
+            } else {
+                lastElementWasIndel = false;
+            }
+        }
+
+        return false;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java
index 2abe7a7a7..099536b40 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java
@@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 /**
  * Filter out reads with low mapping qualities.
@@ -37,10 +36,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 public class BadMateReadFilter implements SamRecordFilter {
 
-    @Argument(fullName = "use_reads_with_bad_mates", shortName = "bad_mates", doc = "Use reads whose mates are mapped excessively far away for calling", required = false)
-    public boolean USE_BADLY_MATED_READS = false;
-
-    public boolean filterOut(SAMRecord rec) {
-        return (!USE_BADLY_MATED_READS && rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
+    public boolean filterOut(final SAMRecord rec) {
+        return (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
     }
 }
\ No newline at end of file