jvarkit

VcfVcf

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

DEPRECATED

obsolete. use GATK

Usage

Usage: vcfvcf [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -AAM
      ALT alleles matters.
      Default: false
    -ACF
      Flag to set if alternate alleles conflict.
    -INFO
      The INFO keys to grab.
      Default: []
    -RAM
      REF allele matters.
      Default: true
    -RID
      Replace the ID field if it exists.
      Default: true
    -RIF
      Replace the INFO field if it exists.
      Default: true
    -TBX
      The VCF file indexed with TABIX. Source of the annotations

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfvcf

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfvcf/VcfVcf.java

Contribute

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

License

The project is licensed under the MIT license.

Citing

Should you cite vcfvcf ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

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