VcfVcf

##Motivation

Get the INFO from a VCF and use it for another VCF.

##Compilation

See also Compilation.

$  make vcfvcf

##Synopsis

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

##Options

TABIX=String
TBX=String                    The VCF file indexed with TABIX. Source of the annotations  Required. 

INFO_IDS=String
INFO=String                   The INFO keys to grab.  This option may be specified 0 or more times. 

REPLACE_INFO_FIELD=Boolean
RIF=Boolean                   Replace the INFO field if it exists.  Default value: true. This option can be set to 
                              'null' to clear the default value. Possible values: {true, false} 

REPLACE_ID=Boolean
RID=Boolean                   Replace the ID field if it exists.  Default value: true. This option can be set to 'null' 
                              to clear the default value. Possible values: {true, false} 

REF_ALLELE_MATTERS=Boolean
RAM=Boolean                   REF allele matters.  Default value: true. This option can be set to 'null' to clear the 
                              default value. Possible values: {true, false} 

ALT_ALLELES_MATTERS=Boolean
AAM=Boolean                   ALT alleles matters.  Default value: false. This option can be set to 'null' to clear the 
                              default value. Possible values: {true, false} 

ALT_CONFLICT_FLAG=String
ACF=String                    Flag to set if alternate alleles conflict.  Default value: null. 

IN=String
I=String                      VCF file/URL to process. Default stdin.   Default value: null. 

OUT=File
O=File                        VCF file to generate. Default stdout.   Default value: null. 

##Source Code

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

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.