Mercurial > repos > iuc > snpeff
annotate readme.rst @ 30:0c8a8cd9dd5b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
| author | iuc |
|---|---|
| date | Sat, 28 Sep 2024 16:27:42 +0000 |
| parents | bbbab2d84e3b |
| children |
| rev | line source |
|---|---|
| 0 | 1 SnpEff wrappers |
| 2 =============== | |
| 3 | |
| 4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani. | |
| 5 It annotates and predicts the effects of variants on genes (such as amino acid changes). | |
| 6 | |
| 7 .. _SnpEff: http://snpeff.sourceforge.net/ | |
| 8 | |
| 9 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. | |
| 10 You can fill this file by running the following command: | |
| 11 | |
| 12 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 | |
| 13 | |
| 14 There are 2 datamanagers to download and install prebuilt SnpEff genome databases: | |
| 15 | |
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bbbab2d84e3b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
iuc
parents:
11
diff
changeset
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16 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeffv_databases.loc`` file |
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bbbab2d84e3b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
iuc
parents:
11
diff
changeset
|
17 * data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeffv_databases.loc`` and adds entries to ``snpeffv_genomedb.loc`` and ``snpeffv_regulationdb.loc`` . |
| 0 | 18 |
| 19 SnpEff citation: |Cingolani2012program|_. | |
| 20 | |
| 21 .. |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 | |
| 22 .. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/ | |
| 23 | |
| 24 SnpSift citation: |Cingolani2012using|_. | |
| 25 | |
| 26 .. |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 | |
| 27 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/ | |
| 28 | |
| 29 Wrapper authors: Jim Johnson |