Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff.xml @ 20:1cae7fb31da7
SnpEffv3.1
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 26 Nov 2012 15:54:26 -0600 |
| parents | aab5e0adb26d |
| children | 4430626bd994 |
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| 19:244c09911d7a | 20:1cae7fb31da7 |
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| 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 by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | 5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> | 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> |
| 7 --> | 7 --> |
| 8 <requirements> | 8 <requirements> |
| 9 <requirement type="package" version="3.0">snpEff</requirement> | 9 <requirement type="package" version="3.1">snpEff</requirement> |
| 10 </requirements> | 10 </requirements> |
| 11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> | 11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> |
| 12 <inputs> | 12 <inputs> |
| 13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | 13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> |
| 14 | 14 |