org.molgenis.data.annotation.core.entity.impl.snpeff

Class SnpEffAnnotator

java.lang.Object

org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator

All Implemented Interfaces:

AnnotatorConfig

@Configuration
public class SnpEffAnnotator
extends Object
implements AnnotatorConfig

SnpEff annotator

SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). see http://snpeff.sourceforge.net/

For this annotator to work SnpEff.jar must be present on the filesystem at the location defined by the RuntimeProperty 'snpeff_jar_location'

new ANN field replacing EFF:

ANN=A|missense_variant|MODERATE|NEXN|NEXN|transcript|NM_144573.3|Coding|8/13|c.733G>A|p.Gly245Arg|1030/3389|733/2028| 245/675||

-lof doesnt seem to work? would be great... http://snpeff.sourceforge.net/snpEff_lof_nmd.pdfs

Field Summary

Fields

Modifier and Type	Field and Description
static String	NAME

Constructor Summary

Constructors

Constructor and Description
SnpEffAnnotator()

Method Summary

Modifier and Type	Method and Description
void	init()
RepositoryAnnotator	snpEff()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAME

public static final String NAME

See Also:

Constant Field Values

Constructor Detail

SnpEffAnnotator

public SnpEffAnnotator()

Method Detail

snpEff

@Bean
public RepositoryAnnotator snpEff()

init

public void init()

Specified by:

init in interface AnnotatorConfig