jvarkit

VCFReplaceTag

Replace the key for INFO/FORMAT/FILTER

DEPRECATED

use bcftools annotate with option -c

Usage

Usage: vcfreplacetag [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
    -k, --tag
      tag to replace . Format FROM/TO
      Default: []
  * -t, --type
      replace type: one of FORMAT,FILTER,INFO
      Default: INFO
    --version
      print version and exit

Keywords

• vcf

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 vcfreplacetag

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/vcfstripannot/VCFReplaceTag.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 vcfreplacetag ? 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

Deprecated

use bcftools annotate with option -c

Example

$   java -jar dist/vcfreplacetag.jar -t INFO -k VDB/NEWNAME ~/jeter.vcf 

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