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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
author Jim Johnson <jj@umn.edu>
date Wed, 27 Nov 2013 09:11:32 -0600
parents 6ad9205c1307
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4:47ddc9f4d0b6 5:8952990fcab9
1 These are galaxy tools for SnpEff ( http://snpeff.sourceforge.net/ ) 1 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).
3 ( http://snpeff.sourceforge.net/ )
2 4
3 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. 5 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.
4 6
5 This will use the default location for genome reference downloads from the snpEff.config: 7 This will use the default location for genome reference downloads from the snpEff.config:
6 data_dir = ~/snpEff/data/ 8 data_dir = ~/snpEff/data/
13 15
14 There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: 16 There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
15 data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc 17 data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc
16 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 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
17 19
20 SnpEff citation:
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]
18 22
23 SnpSift citation:
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.