VcfEnsemblVepRest

##Motivation

Annotate a VCF with the ensembl API.

(I wish I could store a XML or JSON in a VCF... https://github.com/samtools/hts-specs/issues/75 )

##Compilation

See also Compilation.

$  make vcfensemblvep

##Synopsis

$ java -jar dist/vcfensemblvep.jar (stdin|file) 

##Options

Option	Description
-o (fileout)	output. Default: stdout
-s (server)	REST server . Default: http://grch37.rest.ensembl.org
-e (path extension)	Default: stdout/vep/homo_sapiens/region
-n (batch size)	Default: 100
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/ensembl/VcfEnsemblVepRest.java

##Example

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz" |\
gunzip -c  | java -jar dist/vcfensemblvep.jar | grep -v '^#' | cut -f 1,2,4,5,8


1	10583	G	A	VEPTRCSQ=processed_transcript|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328|A|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|A|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675|A|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305|A|SO:0001631,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242|A|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|A|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655|A|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|A|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|A|SO:0001632
1	10611	C	G	VEPTRCSQ=processed_transcript|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328|G|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|G|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675|G|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305|G|SO:0001631,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242|G|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|G|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655|G|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|G|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|G|SO:0001632
1	13302	C	T	VEPTRCSQ=processed_transcript|550|550|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328|T|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|T|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675|T|SO:0001632,transcribed_unprocessed_pseudogene|342|342|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305|T|SO:0001792&SO:0001619,transcribed_unprocessed_pseudogene|543|543|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242|T|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|T|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655|T|SO:0001627&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|T|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|T|SO:0001632
1	13327	G	C	VEPTRCSQ=processed_transcript|575|575|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328|C|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|C|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675|C|SO:0001632,transcribed_unprocessed_pseudogene|367|367|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305|C|SO:0001792&SO:0001619,transcribed_unprocessed_pseudogene|568|568|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242|C|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|C|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655|C|SO:0001627&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|C|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|C|SO:0001632
1	13957	TC	T	VEPTRCSQ=processed_transcript|1206|1206|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328||SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147||SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675||SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305||SO:0001632,transcribed_unprocessed_pseudogene|1199|1199|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242||SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476||SO:0001632,transcribed_unprocessed_pseudogene|1032|1032|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655||SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504||SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562||SO:0001632
1	13980	T	C	VEPTRCSQ=processed_transcript|1228|1228|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000456328|C|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|C|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000541675|C|SO:0001632,transcribed_unprocessed_pseudogene|||||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000450305|C|SO:0001632,transcribed_unprocessed_pseudogene|1221|1221|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000515242|C|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|C|SO:0001632,transcribed_unprocessed_pseudogene|1054|1054|||ENSG00000223972|DDX11L1|HGNC|37102|1|ENST00000518655|C|SO:0001792&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|C|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|C|SO:0001632
1	30923	G	T	VEPTRCSQ=lincRNA|||||ENSG00000243485|MIR1302-10|HGNC|38233|1|ENST00000473358|T|SO:0001627&SO:0001619,lincRNA|||||ENSG00000243485|MIR1302-10|HGNC|38233|1|ENST00000469289|T|SO:0001627&SO:0001619,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000488147|T|SO:0001631,lincRNA|||||ENSG00000237613|FAM138A|HGNC|32334|-1|ENST00000417324|T|SO:0001632,miRNA|||||ENSG00000243485|MIR1302-10|HGNC|38233|1|ENST00000607096|T|SO:0001632,lincRNA|||||ENSG00000237613|FAM138A|HGNC|32334|-1|ENST00000461467|T|SO:0001632,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000538476|T|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000438504|T|SO:0001631,unprocessed_pseudogene|||||ENSG00000227232|WASH7P|HGNC|38034|-1|ENST00000423562|T|SO:0001631
1	46402	C	CTGT	.
1	47190	G	GA	.
1	51476	T	C	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|C|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|C|SO:0001631
1	51479	T	A	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|A|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|A|SO:0001631
1	51914	T	G	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|G|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|G|SO:0001631
1	51935	C	T	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|T|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|T|SO:0001631
1	51954	G	C	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|C|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|C|SO:0001631
1	52058	G	C	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|C|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|C|SO:0001631
1	52144	T	A	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|A|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|A|SO:0001631
1	52185	TTAA	T	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647||SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857||SO:0001631
1	52238	T	G	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|G|SO:0001631,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|G|SO:0001631
[INFO/VcfEnsemblVepRest] 2015-03-19 17:19:04 "done: N=20"
[INFO/VcfEnsemblVepRest] 2015-03-19 17:19:04 "Number of Variants:0"
1	53234	CAT	C	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647||SO:0001627&SO:0001619,unprocessed_pseudogene|763|764|||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857||SO:0001792&SO:0001619
[INFO/VcfEnsemblVepRest] 2015-03-19 17:19:04 "End JOB status=0 [Thu Mar 19 17:19:04 CET 2015] com.github.lindenb.jvarkit.tools.ensembl.VcfEnsemblVepRest done. Elapsed time: 0.05 minutes."
1	54353	C	A	VEPTRCSQ=unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000594647|A|SO:0001627&SO:0001619,unprocessed_pseudogene|||||ENSG00000268020|OR4G4P|HGNC|14822|1|ENST00000606857|A|SO:0001632

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues`
• Source Code: http://github.com/lindenb/jvarkit

##See also

• https://github.com/samtools/hts-specs/issues/75

##History

• 2015 : Creation

License

The project is licensed under the MIT license.