comparison snpSift_annotate.xml @ 20:1cae7fb31da7

SnpEffv3.1
author Jim Johnson <jj@umn.edu>
date Mon, 26 Nov 2012 15:54:26 -0600
parents aab5e0adb26d
children 50c1a8ff6c82
comparison
equal deleted inserted replaced
19:244c09911d7a 20:1cae7fb31da7
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="1.7">SnpSift</requirement> 8 <requirement type="package" version="3.1">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> 10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
11 <inputs> 11 <inputs>
12 <param format="vcf" name="input" type="data" label="VCF input"/> 12 <param format="vcf" name="input" type="data" label="VCF input"/>
13 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 13 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>