jvarkit

NoEmptyVCF

Last commit

If VCF is empty or doesn’t exists, create a dummy one

DEPRECATED

Was developped at the time where VEP didn’t send an output if there was no variant, just a header in the source vcf.

Usage

Usage: noemptyvcf [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output VCF or stdout
    -s, --sample
      Add this genotyped samples
      Default: []
    --version
      print version and exit

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 noemptyvcf

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/misc/NoEmptyVCF.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 noemptyvcf ? 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

History

2017: moved to jcommander

This site is open source. Improve this page.