VCFGeneOntology

Motivation

Finds & filters the GO terms for VCF annotated with SNPEFF or VEP

##Compilation

See also Compilation

ant vcfgo

##Synopsis

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

Options

Option	Description
-A (goa input url)	Default:http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD.
-G (go url)	pDefault:http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz.
-r	remove variant if no GO term is found associated to variant.
-T (string)	pINFO tag. Default:GOA.
-C (Go:Term)	pAdd children to the list of go term to be filtered. Can be used multiple times..
-v	pinverse filter if -C is used..
-F (filter)	pif -C is used, don't remove the variant but set the filter.
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.
--doap	prints a DOAP+XML description of the program and exit

##Source code

main code at: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfgo/VcfGeneOntology.java

Example

INPUT=${HOME}/test.vcf.gz
VCFGO=java -jar dist/vcfgo.jar -A  gene_association.goa_human.gz -G go_daily-termdb.rdf-xml.gz 
DEPS=dist/vcfgo.jar gene_association.goa_human.gz go_daily-termdb.rdf-xml.gz 

all: $(addsuffix .vcf,$(addprefix test,1 2 3 4 5 6 7))
	$(foreach F,$^,echo -e "Output of $F:"  && cat $F; )

test1.vcf: ${DEPS}
	${VCFGO} ${INPUT} |  grep -v "#" | grep GO | cut -f 7,8 | head -n 1 > $@

test2.vcf: ${DEPS}
	${VCFGO}  -T MYGOATAG ${INPUT} |  grep -v "#" | grep MYGOATAG | cut -f 7,8 | head -n 1 > $@
	
test3.vcf: ${DEPS}
	${VCFGO}  -C GO:0007283 ${INPUT} |  grep -v "#" | grep GO  | cut -f 7,8 | head -n 1 > $@
	
test4.vcf: ${DEPS}
	${VCFGO} -C GO:0007283 -v  ${INPUT}|  grep -v "#" |  grep GO | cut -f 7,8 | head -n 1 > $@

test5.vcf: ${DEPS}
	${VCFGO}  -C GO:0007283 -F GOFILTER ${INPUT}| grep -v "#" |   grep GOFILTER | cut -f 7,8 | head -n1 > $@
	
test6.vcf: ${DEPS}
	${VCFGO} -C GO:0007283 -F GOFILTER -v  ${INPUT}| grep -v "#" |   grep GOFILTER | cut -f 7,8 | head -n1 > $@	
	
test7.vcf: ${DEPS}
	${VCFGO} -r ${INPUT} | grep -v "#" | cut -f 7,8 | head -n1 > $@
		
	
gene_association.goa_human.gz :
	curl -o $@ "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD"

go_daily-termdb.rdf-xml.gz :
	curl -o $@ "http://archive.geneontology.org/latest-termdb/$@"

dist/vcfgo.jar:
	ant vcfgo

output of GNU make:

Output of test1.vcf:

.	(...)GOA=AURKAIP1|GO:0070124&GO:0005739&GO:0005515&GO:0070125&GO:0045839&GO:0070126&GO:0032543&GO:0006996&GO:0005743&GO:0005654&GO:0005634&GO:0045862&GO:0043231;MQ=39	GT:PL:DP:GQ	1/1:35,3,0:1:4

Output of test2.vcf:

.	(...)MYGOATAG=AURKAIP1|GO:0070124&GO:0005739&GO:0005515&GO:0070125&GO:0045839&GO:0070126&GO:0032543&GO:0006996&GO:0005743&GO:0005654&GO:0005634&GO:0045862&GO:0043231

Output of test3.vcf:

.	(...)GOA=GJA9|GO:0007154&GO:0005922&GO:0016021,MYCBP|GO:0005739&GO:0005515&GO:0006355&GO:0005813&GO:0005737&GO:0003713&GO:0005634&GO:0007283&GO:0006351;MQ=46

Output of test4.vcf:

.	(...)GOA=AURKAIP1|GO:0070124&GO:0005739&GO:0005515&GO:0070125&GO:0045839&GO:0070126&GO:0032543&GO:0006996&GO:0005743&GO:0005654&GO:0005634&GO:0045862&GO:0043231
```

Output of test5.vcf:

```
GOFILTER	(...)GOA=AURKAIP1|GO:0070124&GO:0005739&GO:0005515&GO:0070125&GO:0045839&GO:0070126&GO:0032543&GO:0006996&GO:0005743&GO:0005654&GO:0005634&GO:0045862&GO:0043231
```

Output of test6.vcf:

```
GOFILTER	(...)GOA=GJA9|GO:0007154&GO:0005922&GO:0016021,MYCBP|GO:0005739&GO:0005515&GO:0006355&GO:0005813&GO:0005737&GO:0003713&GO:0005634&GO:0007283&GO:0006351
```

Output of test7.vcf:

```
.	(...)GOA=AURKAIP1|GO:0070124&GO:0005739&GO:0005515&GO:0070125&GO:0045839&GO:0070126&GO:0032543&GO:0006996&GO:0005743&GO:0005654&GO:0005634&GO:0045862&GO:0043231
```



## Contribute

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

##See also

* 

##History

* 2015 : rewritten, using the htsjdk library
* 2014 : Creation

## License

The project is licensed under the MIT license.