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1 SnpEff wrappers
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2 ===============
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3
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4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani.
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5 It annotates and predicts the effects of variants on genes (such as amino acid changes).
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6
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7 .. _SnpEff: http://snpeff.sourceforge.net/
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9
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10 This repository let you automatically install SnpEff and SnpSift.
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11 This will use the default location for genome reference downloads from the ``snpEff.config`` file:
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12
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13 data_dir = ~/snpEff/data/
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14
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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``.
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16
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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.
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18 You can fill this file by running the following command:
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19
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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
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21
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22 There are 2 datamanagers to download and install prebuilt SnpEff genome databases:
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23
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24 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file
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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``
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26
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27 SnpEff citation: |Cingolani2012program|_.
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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
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30 .. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/
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32 SnpSift citation: |Cingolani2012using|_.
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33
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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
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35 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
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37 Wrapper authors: Jim Johnson
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