diff snpSift_int.xml @ 5:8952990fcab9

Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases

--- a/snpSift_int.xml	Mon Oct 07 10:59:44 2013 -0500
+++ b/snpSift_int.xml	Wed Nov 27 09:11:32 2013 -0600
@@ -1,11 +1,11 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="3.3">
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.4">
 	<description>Filter variants using intervals </description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.3">snpEff</requirement>
+                <requirement type="package" version="3.4">snpEff</requirement>
 	</requirements>
 	<command>
 		java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
@@ -57,5 +57,11 @@
 
 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
 
+SnpEff citation:
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+SnpSift citation:
+"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
+
 	</help>
 </tool>