Difference between revisions of "SnpEff"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Annotation]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|snpeff}} | |{{#vardefine:app|snpeff}} | ||
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: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 | :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 | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - directory with executable scripts |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CONF - directory with the default configuration file. |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | In SnpEff-4.x series the upstream project provides a shell script <code>'snpEff'</code>, which can be used to run the program without calling java directly. | ||
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For snpeff/3.3h we provided a 'snpeff' wrapper that made running snpeff easier. For example, | For snpeff/3.3h we provided a 'snpeff' wrapper that made running snpeff easier. For example, | ||
| − | + | *<pre>java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10</pre> | |
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could be run simply as | could be run simply as | ||
| − | + | *<pre>snpeff download -v athalianaTair10</pre> | |
To override the default 2g java memory setting use the following command on the command-line or in a job script: | To override the default 2g java memory setting use the following command on the command-line or in a job script: | ||
| − | + | *<pre>export _JAVA_OPTIONS="-Xmx4g"</pre> | |
| − | + | |}} | |
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| + | ==Reference Databases== | ||
| + | '''Note:''' we provide a full mirror of snpeff/4.2 reference databases released by the upstream project, so please do not request addition of a new reference database unless you need a custom database built from your data. Please provide a fasta file and an annotation file for building the custom database. | ||
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| + | See the installed database lists for | ||
| + | * [[SnpEff_4.1_Databases|SnpEff-4.1]] | ||
| + | * [[SnpEff_4.2_Databases|SnpEff-4.2]] | ||
| − | + | <!--{{:SnpEff_Databases}}--> | |
<!--PBS scripts--> | <!--PBS scripts--> | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
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{{#if: {{#var: installation}}|==Installation== | {{#if: {{#var: installation}}|==Installation== | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
Latest revision as of 15:19, 5 January 2023
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
Environment Modules
Run module spider snpeff to find out what environment modules are available for this application.
System Variables
- HPC_SNPEFF_DIR - installation directory
- HPC_SNPEFF_BIN - directory with executable scripts
- HPC_SNPEFF_CONF - directory with the default configuration file.
Additional Information
In SnpEff-4.x series the upstream project provides a shell script 'snpEff', which can be used to run the program without calling java directly.
For snpeff/3.3h we provided a 'snpeff' wrapper that made running snpeff easier. For example,
java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10
could 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"
Reference Databases
Note: we provide a full mirror of snpeff/4.2 reference databases released by the upstream project, so please do not request addition of a new reference database unless you need a custom database built from your data. Please provide a fasta file and an annotation file for building the custom database.
See the installed database lists for
Citation
If you publish research that uses snpeff you have to cite it as follows:
SnpEff:
"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:
"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.