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