# HG changeset patch
# User devteam
# Date 1348767617 14400
# Node ID d8bd4326dc3a8a8c83c1db327f7337bfd8898eab
Uploaded
diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpEff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpEff.xml Thu Sep 27 13:40:17 2012 -0400
@@ -0,0 +1,495 @@
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+ Variant effect and annotation
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+ snpEff
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+ 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
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+This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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+For details about this tool, please go to http://snpEff.sourceforge.net
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diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpEff_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpEff_download.xml Thu Sep 27 13:40:17 2012 -0400
@@ -0,0 +1,428 @@
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+ Download a new database
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+ snpEff
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+ java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile
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+This tool downloads a SnpEff database.
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+For details about this tool, please go to http://snpEff.sourceforge.net
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diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpSift_annotate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpSift_annotate.xml Thu Sep 27 13:40:17 2012 -0400
@@ -0,0 +1,32 @@
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+ Annotate SNPs from dbSnp
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+ SnpSift
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+ java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output
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+This is typically used to annotate IDs from dbSnp.
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+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
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diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpSift_caseControl.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpSift_caseControl.xml Thu Sep 27 13:40:17 2012 -0400
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+ Count samples are in 'case' and 'control' groups.
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+ SnpSift
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+ java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
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+Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file.
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+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
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+
diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpSift_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpSift_filter.xml Thu Sep 27 13:40:17 2012 -0400
@@ -0,0 +1,39 @@
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+ Filter variants using arbitrary expressions
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+ SnpSift
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+ java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
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+ $expr
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+You can filter using arbitrary expressions.
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+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
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diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/snpSift_int.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/snpSift_int.xml Thu Sep 27 13:40:17 2012 -0400
@@ -0,0 +1,31 @@
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+ Filter variants using intervals
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+ SnpSift
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+ cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
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+You can filter using intervals (BED file)
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+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
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diff -r 000000000000 -r d8bd4326dc3a snpeff_with_dep-244c09911d7a/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/tool_dependencies.xml Thu Sep 27 13:40:17 2012 -0400
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+ wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff
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+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR/snpEff
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+ $INSTALL_DIR/snpEff/scripts
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+ mkdir SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar
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+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR/SnpSift
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