jvarkit

VcfStats

Produce VCF statitics

Usage

Usage: java -jar dist/vcfstats.jar  [options] Files
Usage: vcfstats [options] Files
  Options:
    -exclude, --exclude
      name of modules to be excluded
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --list
      list available modules and exit
    -o, --output
      Output file. Optional . Default: stdout
    --prefix
      file refix
      Default: <empty string>
    --version
      print version and exit

Keywords

• vcf
• stats
• R

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 vcfstats

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

Creation Date

20131212

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfstats/VcfStats.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfstats/VcfStatsTest.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 vcfstats ? 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

rewritten from scratch 2022

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