Biostar130456

##Motivation

Generate one VCF file for each sample from a multi-samples VCF

##Compilation

See also Compilation.

$ ant biostar130456

##Synopsis

$ java -jar dist/biostar130456.jar -p pattern__SAMPLE__.vcf (stdin|file.vcf) 

##Options

Option	Description
-p (pattern)	output file pattern. Must contain the word __SAMPLE__
-x	remove uncalled genotypes
-z	remove homozygote REF/REF
-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 is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar130456.java

##Example

$   curl -sL "https://raw.githubusercontent.com/arq5x/bedtools2/bc2f97d565c36a82c1a0b12f570fed4398001e5f/test/map/test.vcf" |\
    java -jar dist/biostar130456.jar -x -z -p "sample.__SAMPLE__.vcf.gz" 
sample.NA00003.vcf.gz
sample.NA00001.vcf.gz
sample.NA00002.vcf.gz

$ gunzip -c sample.NA00003.vcf.gz
(...)
##source=myImputationProgramV3.1
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00003
chr1	10	rs6054257	G	A	29	PASS	AF=0.5;DB;DP=14;H2;NS=3	GT:DP:GQ:HQ	1/1:5:43
chr1	20	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DB;DP=10;NS=2	GT:DP:GQ	2/2:4:35
chr1	130	microsat1	GTC	G,GTCT	50	PASS	AA=G;DP=9;NS=3	GT:DP:GQ	1/1:3:40
chr2	130	microsat1	GTC	G,GTCT	50	PASS	AA=G;DP=9;NS=3	GT:DP:GQ	1/1:3:40

Contribute

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

##See also

• VcfMultiToOne
• https://www.biostars.org/p/130456/

##History

• 2015 : Creation

License

The project is licensed under the MIT license.