Mercurial > repos > iuc > snpeff
annotate readme.rst @ 11:bfa6c1b8a03c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 7893b133799b60e1b787262f4649d216adad1fc5
author | iuc |
---|---|
date | Tue, 27 Mar 2018 14:56:29 -0400 |
parents | ce135864629c |
children |
rev | line source |
---|---|
1 | 1 SnpEff wrappers |
2 =============== | |
3 | |
4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani. | |
0 | 5 It annotates and predicts the effects of variants on genes (such as amino acid changes). |
1 | 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: | |
0 | 11 |
1 | 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 | |
8
ce135864629c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
iuc
parents:
7
diff
changeset
|
16 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeffv_databases.loc`` file |
ce135864629c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
iuc
parents:
7
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`` . |
1 | 18 |
19 SnpEff citation: |Cingolani2012program|_. | |
0 | 20 |
1 | 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|_. | |
0 | 25 |
1 | 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/ | |
0 | 28 |
1 | 29 Wrapper authors: Jim Johnson |