Package org.molgenis.data.annotation.impl

Class Summary

Class	Description
CaddServiceAnnotator	This class performs a system call to cross reference a chromosome and genomic location with a tabix indexed file.
ClinicalGenomicsDatabaseServiceAnnotator
ClinVarServiceAnnotator
CosmicServiceAnnotator	This class calls the Ensembl webservice with a ensemble ID.
DbnsfpGeneServiceAnnotator	This class uses a location to retrieve a gene from the ...
DbnsfpVariantServiceAnnotator	This class uses a chromosome to approach a dbNSFP chromosome variant file, it then checks all locations recorded for a chromosome in the data set, for every line, and uses a matching line to add annotation to the data set variant.
EbiServiceAnnotator	This class calls the EBI CHeMBL webservice with a uniprot ID.
ExACServiceAnnotator	ExAC annotator Data @ ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ TODO: feature enhancement: match multiple alternatives from SOURCE file to multiple alternatives in ExAC e.g.
GoNLServiceAnnotator	GoNl annotator data: https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5_with_GTC/ release5_noContam_noChildren_with_AN_AC_GTC_stripped.tgz PLUS chrX from http://molgenis15.target.rug.nl/release4_noContam_noChildren_with_AN_AC_GTC_stripped.tgz GoNL example line: 1 126108 rs146756510 G A .
HgncSymbolServiceAnnotator
KeggServiceAnnotator
OmimHpoAnnotator	Created by jvelde on 2/12/14.
SnpEffServiceAnnotator	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...
ThousandGenomesServiceAnnotator	1000G annotator Data @ http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ TODO: feature enhancement: match multiple alternatives from SOURCE file to multiple alternatives in 1000G e.g.

Enum Summary

Enum	Description
SnpEffServiceAnnotator.impact