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Repository snpsift
Name: snpsift
Owner: iuc
Synopsis: snpEff SnpSift tools from Pablo Cingolani
Variant annotation and effect prediction tools. It annotates and predicts the
effects of variants on genes. There are data managers for the Galaxy admin to
download genome databases.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/snpsift
Type: unrestricted
Revision: 6:2b3e65a4252f
This revision can be installed: True
Times cloned / installed: 1122

Repository README files - may contain important installation or license information

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/ )

This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.

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]

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.

Contents of this repository

Name Description Version Minimum Galaxy Version
Annotate with variant type 4.3+t.galaxy0 16.01
SNPs from dbSnp 4.3+t.galaxy1 16.01
basic checks for VCF specification compliance 4.3+t.galaxy0 16.01
remove INFO field annotations 4.3+t.galaxy0 16.01
Filter variants using intervals 4.3+t.galaxy0 16.01
Filter variants using arbitrary expressions 4.3+t.galaxy0 16.01
Count samples are in 'case' and 'control' groups. 4.3+t.galaxy0 16.01
from a VCF file into a tabular file 4.3+t.galaxy0 16.01

Categories
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA