Biostar130456

##Motivation

Individual VCF files from main VCF file. See https://www.biostars.org/p/13045

##Compilation

Requirements / Dependencies

java 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make > 3.81
curl/wget
git
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar130456

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar130456 standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some paths.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/biostar130456.jar  [options] (stdin|file.vcf|file.vcf.gz)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-p|--pattern (FILEPATTERN) output file pattern. Must contain the word SAMPLE
-x|--uncalled remove uncalled genotypes Default value : "false".
-z|--homref remove homzygote REF/REF Default value : "false".
-h|--help print help
-version|--version show version 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

bash
$   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