VcfCompareCallersOneSample

##Motivation

Description: For my colleague Julien: VCF with one sample called using different callers. *Only keep variant if it was found in min<x=other-files<max

##Compilation

See also Compilation.

$  make vcfcomparecallersonesample

##Synopsis

$ java -jar dist/vcfcomparecallersonesample.jar [options] (stdin|file) 

##Options

Option	Description
-f (file.vcf|vcf.list)	can be specified multiple times. List of VCF to be challenged. Must be sorted on dict. Must contain a dict. Only VCF containing the same sample will be considered. Input file remove itself from the list
-m (int)	min number of challengers found, inclusive. default:0
-M (int)	max number of challengers found, inclusive. default:unbounded
-o (fileout).	Optional. Default: stdout
-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/vcfcmp/VcfCompareCallersOneSample.java

##Example

$ find ./ -name "*.vcf.gz" > vcf.list
$  java -jar dist/VcfCompareCallersOneSample.jar -f vcf.list in.vcf.gz > out.vcf

Contribute

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

##See also

##History

• 2015 : Creation

License

The project is licensed under the MIT license.