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Repository snpeff
Name: snpeff
Owner: iuc
Synopsis: SnpEff is a genetic variant annotation and effect prediction toolbox
Variant annotation and effect prediction tools. It annotates and
predicts the effects of variants on genes. There
are data managers for tha Galaxy admin to download genome databases.
Content homepage: http://snpeff.sourceforge.net/
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/snpeff
Type: unrestricted
Revision: 20:8f92c2b26e6d
This revision can be installed: True
Times cloned / installed: 2515

Repository README files - may contain important installation or license information

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).

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:

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/snpeffv_databases.loc file
  • 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 .

SnpEff citation: 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.

SnpSift citation: 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.

Wrapper authors: Jim Johnson

Contents of this repository

Name Description Version Minimum Galaxy Version
database from Genbank or GFF record 4.3+T.galaxy3 16.01
list chromosome names/lengths 4.3+T.galaxy1 16.01
download a pre-built database 4.3+T.galaxy2 16.01
annotate variants 4.3+T.galaxy1 16.01
list available databases 4.3+T.galaxy1 16.01

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