SnpEff

Description

snpeff website  

SnpEff

Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Features

• Supports over 8,500 genomes.
• Cancer variants analysis
• GATK compatibile (-o gatk)
• HGSV notations support (clinical)

SnpSift

SnpSift helps filtering and manipulating genomic annotated files (VCF). Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants

Required Modules

Serial

• snpeff

System Variables

• HPC_{{#uppercase:snpeff}}_DIR

Additional Information

We provide a 'snpeff' wrapper that makes running snpeff easier. For example,

java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10

can be run simply as

snpeff download -v athalianaTair10

To override the default 2g java memory setting use the following command on the command-line or in a job script:

export _JAVA_OPTIONS="-Xmx4g"