diff --git a/test-data/filter1_in5.tab b/test-data/filter1_in5.tab
new file mode 100644
index 00000000000..9bf6d18fb14
--- /dev/null
+++ b/test-data/filter1_in5.tab
@@ -0,0 +1,5 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	replicate 1_FPKM	replicate 1_conf_lo	replicate 1_conf_hi	replicate 1_status	replicate 2_FPKM	replicate 2_conf_lo	replicate 2_conf_hi	replicate 2_status
+CUFF.1.1	-	-	CUFF.1	-	-	chr19:305598-306225	627	-	0	0	0	OK	206.177	0	694.583	OK
+CUFF.10.1	-	-	CUFF.10	-	-	chr19:618402-618611	209	-	0	0	0	OK	767.201	0	2801.16	OK
+CUFF.100.1	-	-	CUFF.100	-	-	chr19:1625589-1652356	888	-	0	0	0	OK	172.566	0	2879.98	OK
+CUFF.100.2	-	-	CUFF.100	-	-	chr19:1625589-1652356	581	-	0	0	0	OK	1147.8	0	5922.31	OK
diff --git a/test-data/filter1_test5.tab b/test-data/filter1_test5.tab
new file mode 100644
index 00000000000..785309afe58
--- /dev/null
+++ b/test-data/filter1_test5.tab
@@ -0,0 +1,4 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	replicate 1_FPKM	replicate 1_conf_lo	replicate 1_conf_hi	replicate 1_status	replicate 2_FPKM	replicate 2_conf_lo	replicate 2_conf_hi	replicate 2_status
+CUFF.1.1	-	-	CUFF.1	-	-	chr19:305598-306225	627	-	0	0	0	OK	206.177	0	694.583	OK
+CUFF.100.1	-	-	CUFF.100	-	-	chr19:1625589-1652356	888	-	0	0	0	OK	172.566	0	2879.98	OK
+CUFF.100.2	-	-	CUFF.100	-	-	chr19:1625589-1652356	581	-	0	0	0	OK	1147.8	0	5922.31	OK
diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py
index f78da20fe1c..80b6e51d145 100644
--- a/tools/stats/filtering.py
+++ b/tools/stats/filtering.py
@@ -36,6 +36,7 @@ try:
     in_column_types = sys.argv[5].split( ',' )
 except:
     stop_err( "Data does not appear to be tabular.  This tool can only be used with tab-delimited data." )
+num_header_lines = int( sys.argv[6] )
 
 # Unescape if input has been escaped
 mapped_str = {
@@ -98,6 +99,12 @@ code = '''
 for i, line in enumerate( file( in_fname ) ):
     total_lines += 1
     line = line.rstrip( '\\r\\n' )
+
+    if i < num_header_lines:
+        lines_kept += 1
+        print >> out, line
+        continue
+
     if not line or line.startswith( '#' ):
         skipped_lines += 1
         continue
diff --git a/tools/stats/filtering.xml b/tools/stats/filtering.xml
index bcb83039850..a71481fb473 100644
--- a/tools/stats/filtering.xml
+++ b/tools/stats/filtering.xml
@@ -1,13 +1,14 @@
 <tool id="Filter1" name="Filter" version="1.1.0">
   <description>data on any column using simple expressions</description>
   <command interpreter="python">
-    filtering.py $input $out_file1 "$cond" ${input.metadata.columns} "${input.metadata.column_types}"
+    filtering.py $input $out_file1 "$cond" ${input.metadata.columns} "${input.metadata.column_types}" $header_lines
   </command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Filter" help="Dataset missing? See TIP below."/>
     <param name="cond" size="40" type="text" value="c1=='chr22'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool.">
       <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/>
     </param>
+    <param name="header_lines" type="integer" value="0" label="Number of header lines to skip"/>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input"/>
@@ -16,24 +17,34 @@
     <test>
       <param name="input" value="1.bed"/>
       <param name="cond" value="c1=='chr22'"/>
+      <param name="header_lines" value="0"/>
       <output name="out_file1" file="filter1_test1.bed"/>
     </test>
     <test>
       <param name="input" value="7.bed"/>
       <param name="cond" value="c1=='chr1' and c3-c2>=2000 and c6=='+'"/>
+      <param name="header_lines" value="0"/>
       <output name="out_file1" file="filter1_test2.bed"/>
     </test>
     <!-- Test filtering of file with a variable number of columns. -->
     <test>
       <param name="input" value="filter1_in3.sam"/>
       <param name="cond" value="c3=='chr1' and c5>5"/>
+      <param name="header_lines" value="0"/>
       <output name="out_file1" file="filter1_test3.sam"/>
     </test>
     <test>
       <param name="input" value="filter1_inbad.bed"/>
       <param name="cond" value="c1=='chr22'"/>
+      <param name="header_lines" value="0"/>
       <output name="out_file1" file="filter1_test4.bed"/>
     </test>
+    <test>
+      <param name="input" value="filter1_in5.tab"/>
+      <param name="cond" value="c8>500"/>
+      <param name="header_lines" value="1"/>
+      <output name="out_file1" file="filter1_test5.tab"/>
+    </test>
   </tests>
   <help>