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diff snpSift_caseControl.xml @ 5:8952990fcab9

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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
author Jim Johnson <jj@umn.edu>
date Wed, 27 Nov 2013 09:11:32 -0600
parents 6ad9205c1307
children 0ad9733e22a4
line wrap: on
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--- a/snpSift_caseControl.xml	Mon Oct 07 10:59:44 2013 -0500
+++ b/snpSift_caseControl.xml	Wed Nov 27 09:11:32 2013 -0600
@@ -1,11 +1,11 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.3">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4">
   <description>Count samples are in 'case' and 'control' groups.</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 -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
@@ -121,5 +121,13 @@
 
 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
+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>