--- a/README.txt	Mon Aug 03 05:03:16 2015 -0400
+++ b/README.txt	Mon Aug 03 05:45:16 2015 -0400
@@ -7,7 +7,7 @@
    - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system
      (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ )
      
-   - change "/path/to/VN_genomes_varfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics
+   - change "/path/to/VN_genomes_varfiles_lists_hg18" to the location of the directory containing files with the locations of all the Complete Genomics
      varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g.
      
 	    /path/to/normal-varfile-1
@@ -20,10 +20,44 @@
 		/path/to/normal-varfile-8
    			...
    			
-   	 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
+   - edit the tool xml file to offer sets of virtual normals
+
+	[..]
+		<!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
+		<param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples, for hg18 54 genomes will be used.">
+			<option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option>
+			<option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
+			<option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
+                        <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
+		</param>
+	[..]
+
+	the values indicate files expected to be at the location configured in the loc file, 
+
+
+     So if your .loc file looks like this:
+
+
+		#loc file for annovar tool
+
+		# <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns>
+
+		hg18	hg18	Virtual Normal hg18	/path/to/VN_genomes_varfiles_lists_hg18	/path/to/VN_genomes_junctionfiles_lists_hg18	/path/to/hg18.crr
+		hg19	hg19	Virtual_Normal hg19	/path/to/VN_genomes_varfiles_lists_hg19	/path/to/VN_genomes_junctionfiles_lists_hg19	/path/to/hg19.crr
+
+     And your xml file like the example above, then the tool expects the following files to exist:
+		 /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt 	
+     		 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt
+		etc
+     and containing a 1-per-line list of locations of the varfiles of the normal genomes.
+
+
+ 
+
+     Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
      (can be downloaded from ftp://ftp2.completegenomics.com/)		
    
-   - change	"/path/to/VN_genomes_junctionfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics
+   - change	"/path/to/VN_genomes_junctionfiles_lists_hg18" to the location of the file containing the locations of all the Complete Genomics
      junctionfiles to be used as a virtual normal. This file should contain 1 file location per line.  For example, Complete Genomics' 
 	 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/)