diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index 3dda674007587fe9277cdfe972408b34aad0e937..4d095fe1bc0c4fabcd24893064bbc268bdd2a1c9 100644
--- a/docs/file_menu.sgml
+++ b/docs/file_menu.sgml
@@ -72,7 +72,7 @@ the user.
   </SECT2>
 
   <SECT2 ID="FILEMENU-READ-BAM">
-    <TITLE>Read BAM ...</TITLE>
+    <TITLE>Read BAM / VCF ...</TITLE>
      <PARA>
 Read a BAM file that has been sorted and indexed using <ULINK 
 URL="http://samtools.sourceforge.net/">samtools</ULINK>. This provides an integrated
@@ -81,10 +81,46 @@ sequence alignment mappings to a reference sequence. This require Artemis to
 be run with Java 1.6 as it makes use of <ULINK URL="http://picard.sourceforge.net/">
 picard</ULINK> to read from the BAM file.
       </PARA>
+      <PARA>
+Variant Call Format (<ULINK
+URL="http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0">VCF</ULINK>) 
+files can also be read. The VCF files need to be compressed and indexed using bgzip and 
+tabix respectively (see the <ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK> and 
+<ULINK URL="http://sourceforge.net/projects/samtools/files/">download page</ULINK>).
+The compressed file gets read in (e.g. file.vcf.gz) and below are the commands for 
+generating this from a VCF file:
+	</PARA>
+	<SYNOPSIS>
+	bgzip file.vcf
+	tabix -p vcf file.vcf.gz
+	</SYNOPSIS>
+	<PARA>
+As with reading in multiple BAM files, it is possible to read a number of (compressed and indexed)
+VCF files by listing their full paths in a single file. They then get displayed in separate rows 
+in the VCF panel.
+	</PARA>
+	<MEDIAOBJECT>
+	<IMAGEOBJECT>
+	   <IMAGEDATA FORMAT="png" FILEREF="vcf.png"></IMAGEOBJECT>
+	</MEDIAOBJECT>
+ 	<PARA>
+For single base changes the colour represents the base it is being changed to, i.e. T black,
+G blue, A green, C red. There are options available to filter the display by the different 
+types of variantions. Right clicking on the VCF panel will display a pop-up menu in which 
+it is possible to select to hide or show synonymous, non-synonymous, deletion (grey), 
+insertion (yellow), and multiple allele (orange line with a circle at the top) 
+variants.  From this menu it is also possible to hide the variants that do not overlap CDS 
+features. There is an option to mark variants that introduce stop codons (into the CDS 
+features) with a circle in the middle of the line that represents the variant. There is also 
+an option to filter by the quality score.
+    	</PARA>
+	<PARA>
+Placing the mouse over a vertical line shows an overview  of the variation as a 
+tooltip. Also right clicking over a line then gives an extra option in the pop-up
+menu to show the details for that variation in a separate window.
+	</PARA>
   </SECT2>
 
-
-
   <SECT2 ID="FILEMENU-SAVE-DEFAULT-ENTRY">
     <TITLE>Save Default Entry</TITLE>
     <PARA>