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annotate readme.rst @ 11:c5288d5a446e

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Update to version 3.6 and refactor to new repositories: snpsift, snpeff_datatypes, data_manager_snpeff
author Jim Johnson <jj@umn.edu>
date Thu, 26 Jun 2014 08:40:30 -0500
parents aecbd8878923
children 6d429d880a75
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1 These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani.
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2 It annotates and predicts the effects of variants on genes (such as amino acid changes).
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3 ( http://snpeff.sourceforge.net/ )
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5 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.
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7 The genome reference options used by the tools:
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8 "SnpEff" snpEff.xml
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9 "SnpEff Download" snpEff_download.xml
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10 are taken from: tool-data/snpeffect_genomedb.loc
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12 SnpEff citation:
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13 "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]
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15 SnpSift citation:
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16 "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.