Difference between revisions of "SnpEff"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{#uppercase:{{#var:app}}}}_DIR | + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - main installation directory |
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - directory with executable scripts | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_CONF - directory with the default configuration file. | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 16:41, 19 August 2013
Description
- 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 - main installation directory
- HPC_{{#uppercase:snpeff}}_BIN - directory with executable scripts
- HPC_{{#uppercase:snpeff}}_CONF - directory with the default configuration file.
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"