--- a/snpSift_filter.xml	Thu Jan 17 16:31:12 2013 -0500
+++ b/snpSift_filter.xml	Wed Jan 30 16:20:32 2013 -0600
@@ -31,9 +31,34 @@
         </stdio>
 	<help>
 
-You can filter using arbitrary expressions.
+**SnpSift filter**
+
+You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
+
+Some examples:
+
+  - *I want to filter out samples with quality less than 30*:
+
+    * **( QUAL &gt; 30 )**
+
+  - *...but we also want InDels that have quality 20 or more*:
+
+    * **(( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
 
-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
+  - *...or any homozygous variant present in more than 3 samples*:
+
+    * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
+
+  - *...or any heterozygous sample with coverage 25 or more*:
+
+    * **((countHet() > 0) &amp;&amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
+
+  - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
+
+    * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**
+
+
+For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
 
 	</help>
 </tool>