Mercurial > repos > iuc > snpeff
diff readme.rst @ 1:500832f27cbc draft
Uploaded
author | iuc |
---|---|
date | Thu, 22 Jan 2015 08:28:37 -0500 |
parents | e8adfc4c0a6b |
children | 7adfd0589f49 |
line wrap: on
line diff
--- a/readme.rst Wed Dec 11 08:53:32 2013 -0500 +++ b/readme.rst Thu Jan 22 08:28:37 2015 -0500 @@ -1,24 +1,38 @@ -These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. +SnpEff wrappers +=============== + +These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani. It annotates and predicts the effects of variants on genes (such as amino acid changes). -( http://snpeff.sourceforge.net/ ) + +.. _SnpEff: http://snpeff.sourceforge.net/ + -This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. +This repository let you automatically install SnpEff and SnpSift. +This will use the default location for genome reference downloads from the ``snpEff.config`` file: + + data_dir = ~/snpEff/data/ -This will use the default location for genome reference downloads from the snpEff.config: -data_dir = ~/snpEff/data/ -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. +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``. + +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. +You can fill this file by running the following command: -The genome reference options used by the tools: - "SnpEff" snpEff.xml - "SnpEff Download" snpEff_download.xml -are taken from: tool-data/snpeffect_genomedb.loc + 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 + +There are 2 datamanagers to download and install prebuilt SnpEff genome databases: + +* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file +* 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`` + +SnpEff citation: |Cingolani2012program|_. -There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: - data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc - 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 +.. |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 +.. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/ + +SnpSift citation: |Cingolani2012using|_. -SnpEff citation: -"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] +.. |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 +.. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/ -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, 2012. +Wrapper authors: Jim Johnson +