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date Thu, 22 Jan 2015 08:28:37 -0500
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1 These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. 1 SnpEff wrappers
2 ===============
3
4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani.
2 It annotates and predicts the effects of variants on genes (such as amino acid changes). 5 It annotates and predicts the effects of variants on genes (such as amino acid changes).
3 ( http://snpeff.sourceforge.net/ )
4 6
5 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. 7 .. _SnpEff: http://snpeff.sourceforge.net/
6 8
7 This will use the default location for genome reference downloads from the snpEff.config:
8 data_dir = ~/snpEff/data/
9 You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff.
10 9
11 The genome reference options used by the tools: 10 This repository let you automatically install SnpEff and SnpSift.
12 "SnpEff" snpEff.xml 11 This will use the default location for genome reference downloads from the ``snpEff.config`` file:
13 "SnpEff Download" snpEff_download.xml
14 are taken from: tool-data/snpeffect_genomedb.loc
15 12
16 There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: 13 data_dir = ~/snpEff/data/
17 data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc
18 data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc
19 14
20 SnpEff citation: 15 You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``.
21 "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]
22 16
23 SnpSift citation: 17 The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file.
24 "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. 18 You can fill this file by running the following command:
19
20 java -jar snpEff.jar databases | tail -n +3 | cut -f 1,2 | awk '{ gsub(/_/, " ", $2); printf "%s\\t%s : %s\\n", $1, $2, $1 }' | sort -k 2 > snpeffect_genomedb.loc
21
22 There are 2 datamanagers to download and install prebuilt SnpEff genome databases:
23
24 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file
25 * data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc``
26
27 SnpEff citation: |Cingolani2012program|_.
28
29 .. |Cingolani2012program| replace:: Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., Ruden, D. M. (2012) 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. *Fly* 6(2):80-92
30 .. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/
31
32 SnpSift citation: |Cingolani2012using|_.
33
34 .. |Cingolani2012using| replace:: Cingolani, P., Patel, V. M., Coon, M., Nguyen, T., Land, S. J., Ruden, D. M., Lu, X. (2012) Using *Drosophila melanogaster* as a model for genotoxic chemical mutational studies with a new program, SnpSift. *Front. Genet.* 3:35
35 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
36
37 Wrapper authors: Jim Johnson
38