# HG changeset patch
# User iuc
# Date 1421935081 18000
# Node ID 9e6fa49c107796608b19a14715f5d750f7815bec
Uploaded
diff -r 000000000000 -r 9e6fa49c1077 snpSift_geneSets.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_geneSets.xml Thu Jan 22 08:58:01 2015 -0500
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+ Annotating GeneSets, such as Gene Ontology, KEGG, Reactome
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+ snpSift_macros.xml
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+ java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
+ #if $db_opts.db_opts_selector == "db"
+ "${db_opts.database.fields.path}"
+ #elif $db_opts.db_opts_selector == "histdb"
+ "$db_opts.histdb"
+ #end if
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+ $input 2> $log > $output
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+This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome.
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+.. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
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+.. class:: warningmark
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+The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.
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+@EXTERNAL_DOCUMENTATION@
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+@CITATION_SECTION@
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+For `MSigDB`_, please cite |Subramanian2005|_.
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+.. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
+.. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550
+.. _Subramanian2005: http://www.pnas.org/content/102/43/15545
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+ 10.1073/pnas.0506580102
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diff -r 000000000000 -r 9e6fa49c1077 snpSift_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_macros.xml Thu Jan 22 08:58:01 2015 -0500
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+ snpEff
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+For details about this tool, please go to:
+ http://snpeff.sourceforge.net/SnpEff_manual.html
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+
+ ------
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+**Citation**
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+For the underlying tool, please cite the following two publications:
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+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, 3:35, 2012.
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+ 10.3389/fgene.2012.00035
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diff -r 000000000000 -r 9e6fa49c1077 tool-data/snpeff_msigdb_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff_msigdb_database.loc.sample Thu Jan 22 08:58:01 2015 -0500
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+## Molecular Signatures Database (MSigDB) for SnpEff.
+## You can download MSigDb from http://www.broadinstitute.org/gsea/msigdb
+#msigdb_id msigdb_name path_to_database
+#msigdb_08_2014 MSigDB 08-2014 /data/msigdb/08_2014/msigdb.gmt
diff -r 000000000000 -r 9e6fa49c1077 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Jan 22 08:58:01 2015 -0500
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diff -r 000000000000 -r 9e6fa49c1077 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jan 22 08:58:01 2015 -0500
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