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comparison 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
comparison
equal deleted inserted replaced
4:47ddc9f4d0b6 5:8952990fcab9
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.3"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4">
2 <description>Count samples are in 'case' and 'control' groups.</description> 2 <description>Count samples are in 'case' and 'control' groups.</description>
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 4 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.3">snpEff</requirement> 8 <requirement type="package" version="3.4">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
12 #if $name.__str__.strip() != '': 12 #if $name.__str__.strip() != '':
13 -name $name 13 -name $name
119 - Case / Control column designation = ""++++------" 119 - Case / Control column designation = ""++++------"
120 120
121 121
122 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol 122 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
123 123
124 SnpEff citation:
125 "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]
126
127 SnpSift citation:
128 "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.
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124 </help> 132 </help>
125 </tool> 133 </tool>